├── bin └── .gitignore ├── src ├── Plugins │ └── .gitignore ├── Resources │ ├── Icons │ │ ├── Seg3D.rc │ │ ├── Seg3D.icns │ │ ├── seg3d2_128.ico │ │ ├── seg3d2_128.png │ │ ├── seg3d2_16.ico │ │ ├── seg3d2_256.ico │ │ ├── seg3d2_256.png │ │ ├── seg3d2_32.ico │ │ └── seg3d2_48.ico │ ├── Images │ │ ├── Symbol.png │ │ ├── HelpWhite.png │ │ ├── Seg3DSplash.png │ │ ├── VisibleGray.png │ │ ├── VisibleOff.png │ │ ├── VisibleWhite.png │ │ ├── DownArrowWhite.png │ │ ├── LabelMapWhite.png │ │ ├── RightArrowWhite.png │ │ └── IsosurfaceVisibleGrey.png │ ├── Footer_Icons │ │ ├── new.png │ │ ├── footer_01.png │ │ └── switch_tool.png │ ├── General_Icons │ │ ├── exit.png │ │ ├── Progress0.png │ │ ├── Progress20.png │ │ ├── Progress40.png │ │ ├── Progress60.png │ │ ├── Progress80.png │ │ ├── arrow-down.png │ │ ├── arrow-up.png │ │ ├── maximize.png │ │ ├── radio-fill.png │ │ ├── Progress100.png │ │ ├── Progress120.png │ │ ├── Progress140.png │ │ ├── Progress160.png │ │ ├── Progress180.png │ │ ├── Progress200.png │ │ ├── Progress220.png │ │ ├── Progress240.png │ │ ├── Progress260.png │ │ ├── Progress280.png │ │ ├── Progress300.png │ │ ├── Progress320.png │ │ ├── Progress340.png │ │ ├── arrow-expand.png │ │ ├── arrow-right.png │ │ ├── radio-empty.png │ │ ├── arrow-expanded.png │ │ ├── checkbox-selected.png │ │ ├── checkbox-unselected.png │ │ └── checkbox-indeterminate.png │ ├── Palette_Icons │ │ ├── add_01.png │ │ ├── info_01.png │ │ ├── isoX_01.png │ │ ├── iso_01.png │ │ ├── layers.png │ │ ├── lock_01.png │ │ ├── lock_03.png │ │ ├── brush_01.png │ │ ├── isoGo_01.png │ │ ├── isoMenu_01.png │ │ ├── minus_01.png │ │ ├── opacity_01.png │ │ ├── windowed.png │ │ ├── duplicate_01.png │ │ ├── visibility_01.png │ │ ├── color_transparent.png │ │ ├── mask_transparent.png │ │ ├── visibilityPlus_01.png │ │ ├── mask_bitplane_1248.png │ │ └── mask_label_map_1234.png │ ├── Viewport_Icons │ │ ├── ISO_01.png │ │ ├── axisV.png │ │ ├── axisX.png │ │ ├── axisY.png │ │ ├── axisZ.png │ │ ├── cut_01.png │ │ ├── center_01.png │ │ ├── grid_01.png │ │ ├── lock_01.png │ │ ├── pick_01.png │ │ ├── planes_01.png │ │ ├── snap_01.png │ │ ├── lighting_01.png │ │ ├── viewData_01.png │ │ ├── perspective_01.png │ │ ├── visibility_01.png │ │ ├── wireframe_01.png │ │ ├── flipVertical_01.png │ │ ├── flipHorizontal_01.png │ │ ├── showSlicePlanes_01.png │ │ ├── viewCrosshairs_01.png │ │ └── volumeRendering_01.png │ └── info.plist ├── ThirdParty │ └── tinyxml │ │ ├── changes.txt │ │ └── tinystr.cpp ├── Application │ ├── Tools │ │ └── MeasurementTool.cc │ ├── Renderer │ │ ├── OrientationArrowsShader.frag │ │ ├── OrientationArrowsShader.vert │ │ ├── Fog.vert │ │ ├── Fog.frag │ │ ├── SliceShader.vert │ │ ├── IsosurfaceShader.frag │ │ ├── IsosurfaceShader.vert │ │ ├── Lighting.vert │ │ └── Lighting.frag │ └── Filters │ │ └── Utils │ │ └── PadValues.cc ├── Documentation │ ├── presentations │ │ ├── Seg3DInsights.ppt │ │ └── Seg3DVisInsights.ppt │ ├── Seg3DTutorial_figures │ │ ├── maskdata.png │ │ ├── AngioData.png │ │ ├── CannyAfter.png │ │ ├── LoadVolume.png │ │ ├── OtsuAfter.png │ │ ├── OtsuBefore.png │ │ ├── Speedline.png │ │ ├── paintlumen.png │ │ ├── CannyBefore.png │ │ ├── LoadVolume_2.png │ │ ├── MaskDataBrain.png │ │ ├── SpeedlineFill.png │ │ ├── polylinelumen.png │ │ ├── MainSeg3DWindow.png │ │ ├── MaskedPainting.png │ │ ├── Neighborhood_1.png │ │ ├── SpeedlineImage.png │ │ ├── ThresholdAngio.png │ │ ├── welcome_screen.png │ │ ├── FilteredAngioData.png │ │ ├── KeyboardShortcuts.png │ │ ├── SkullSegmentation.png │ │ ├── creatingisosurface.png │ │ ├── logicaloperators.png │ │ ├── LoadingBrainDataSet.png │ │ ├── LoadingSegmentation.png │ │ ├── ThresholdGreyMatter.png │ │ ├── ThresholdWHiteMatter.png │ │ ├── polylinesuperficial.png │ │ ├── Cannywithmeanandlayers.png │ │ ├── Median-ImageCorrected.png │ │ └── NeighborhoodConnected.png │ └── Seg3DBasicFunctionality_figures │ │ ├── Add.png │ │ ├── New.png │ │ ├── Close.png │ │ ├── Data.png │ │ ├── Mask.png │ │ ├── Minus.png │ │ ├── dock.png │ │ ├── AlignOff.png │ │ ├── ClipOff.png │ │ ├── FogOff.png │ │ ├── FogPanel.png │ │ ├── GridOff.png │ │ ├── InfoOff.png │ │ ├── LightOff.png │ │ ├── LockOff.png │ │ ├── Pref_gen.png │ │ ├── TextOff.png │ │ ├── WorldOff.png │ │ ├── layout.png │ │ ├── DownArrow.png │ │ ├── ExportSeg.png │ │ ├── OpacityOff.png │ │ ├── OverlayOff.png │ │ ├── PickingOff.png │ │ ├── Pref_side.png │ │ ├── Pref_view.png │ │ ├── RightArrow.png │ │ ├── SwitchTool.png │ │ ├── ToolWindow.png │ │ ├── VisibleOff.png │ │ ├── VolRendOpt.png │ │ ├── close_dock.png │ │ ├── newProject.png │ │ ├── quick_menu.png │ │ ├── AppearanceOff.png │ │ ├── AutoViewOff.png │ │ ├── ClippingPanel.png │ │ ├── DuplicateOff.png │ │ ├── ExportSeg_2.png │ │ ├── FlipHorizOff.png │ │ ├── FlipVertOff.png │ │ ├── ImportWidget.png │ │ ├── LayerOpacity.png │ │ ├── LayerWindow.png │ │ ├── Pref_layers.png │ │ ├── ProjectWindow.png │ │ ├── ProvenanceOff.png │ │ ├── Seg3D_layout.png │ │ ├── VolRendPanel.png │ │ ├── close_window.png │ │ ├── layout_blank.pdf │ │ ├── layout_blank.png │ │ ├── LayerAppearance.png │ │ ├── PickingLinesOff.png │ │ ├── geometric_info.png │ │ ├── welcome_screen.png │ │ ├── IsosurfaceMenuOff.png │ │ ├── PreviousSliceOff.png │ │ ├── ProvenanceWindow.png │ │ ├── SlicesVisibleOff.png │ │ ├── VolumeRenderingOff.png │ │ ├── VolumeVisibleOff.png │ │ ├── Controller_EventLog.png │ │ ├── Controller_OnStartup.png │ │ ├── Controller_OpenTool.png │ │ ├── IsosurfaceComputeOff.png │ │ ├── IsosurfaceDeleteOff.png │ │ ├── IsosurfaceVisibleOff.png │ │ ├── PythonConsole_blank.png │ │ ├── Controller_ActionList.png │ │ ├── Controller_UsabilityMsg.png │ │ ├── Controller_StateVariables.png │ │ ├── Controller_ToolStateVars.png │ │ └── InvisibleSlicesVisibleOff.png ├── CMake │ ├── ReadMe.txt │ ├── Welcome.txt │ ├── Scripts │ │ ├── build_full_static_lib.bat.in │ │ └── repair_package.sh.in │ ├── Modules │ │ └── CPack.Distribution.dist.in │ ├── License.txt │ └── GetGitRevisionDescription.cmake.in ├── Configuration │ └── ActionPythonWrapperFunctionSource.in ├── BuildNotes.txt ├── Main │ └── Seg3DLib │ │ ├── Seg3DLib_example_main.cc │ │ └── Lib │ │ └── Seg3D_lib.h ├── License.txt ├── Core │ ├── VolumeRenderer │ │ ├── VolumeShaderOcclusion.vert │ │ └── VolumeShaderSimple.vert │ ├── Renderer │ │ └── Limits.h │ ├── Utils │ │ └── Notifier.cc │ ├── Python │ │ └── ToPythonConverters.h │ ├── DataBlock │ │ ├── ITKImageData.cc │ │ └── ITKImage2DData.cc │ ├── RenderResources │ │ ├── RenderContext.cc │ │ └── RenderResourcesContext.cc │ ├── Action │ │ └── ActionParameter.cc │ └── State │ │ └── StateViewBase.cc ├── Bootstrap │ ├── CMakeLists.txt │ └── ShaderImporter │ │ └── CMakeLists.txt ├── QtUtils │ └── CMakeLists.txt └── Interface │ └── CMakeLists.txt ├── docs ├── _static │ ├── css │ │ └── main.css │ └── seg3d.png ├── bib.rst ├── user_docs │ ├── Tools │ │ ├── images │ │ │ ├── hr.png │ │ │ ├── CropGUI.png │ │ │ ├── MeanGUI.png │ │ │ ├── PadGUI.png │ │ │ ├── body-bg.png │ │ │ ├── checker.png │ │ │ ├── InvertGUI.png │ │ │ ├── MeasureGUI.png │ │ │ ├── MedianGUI.png │ │ │ ├── zip-icon.png │ │ │ ├── BooleanORGUI.png │ │ │ ├── CannyEdgeGUI.png │ │ │ ├── CopyPasteGUI.png │ │ │ ├── FillHolesGUI.png │ │ │ ├── MaskDataGUI.png │ │ │ ├── PolylineGUI.png │ │ │ ├── ResampleGUI.png │ │ │ ├── SpeedlineGUI.png │ │ │ ├── ThresholdGUI.png │ │ │ ├── TransformGUI.png │ │ │ ├── highlight-bg.jpg │ │ │ ├── octocat-icon.png │ │ │ ├── tar-gz-icon.png │ │ │ ├── ArithmeticGUI.png │ │ │ ├── BooleanANDGUI.png │ │ │ ├── BooleanXORGUI.png │ │ │ ├── DistanceMapGUI.png │ │ │ ├── FlipRotateGUI.png │ │ │ ├── GaussianBlurGUI.png │ │ │ ├── PaintBrushGUI.png │ │ │ ├── SelectPointsGUI.png │ │ │ ├── BooleanRemoveGUI.png │ │ │ ├── OtsuThresholdGUI.png │ │ │ ├── ExtractDataLayersGUI.png │ │ │ ├── PointSetRegisterGUI.png │ │ │ ├── ConfidenceConnectedGUI.png │ │ │ ├── ConnectedComponentGUI.png │ │ │ ├── IntensityCorrectionGUI.png │ │ │ ├── ConnectedComponentSizeGUI.png │ │ │ ├── FastBinaryDilateErodeGUI.png │ │ │ ├── HistogramEqualizationGUI.png │ │ │ ├── NeighborhoodConnectedGUI.png │ │ │ ├── SegmentationLevelSetGUI.png │ │ │ ├── SmoothBinaryDilateErodeGUI.png │ │ │ ├── CurvatureAnisotropicDiffusionGUI.png │ │ │ └── GradientAnisotropicDiffusionGUI.png │ │ ├── Tools │ │ │ ├── index.rst │ │ │ ├── SelectPointsTool.md │ │ │ ├── InvertTool.md │ │ │ ├── PadTool.md │ │ │ ├── FlipRotateTool.md │ │ │ ├── CropTool.md │ │ │ ├── TransformTool.md │ │ │ ├── ResampleTool.md │ │ │ ├── PointSetRegistrationTool.md │ │ │ └── MeasurementTool.md │ │ ├── DataFilters │ │ │ ├── index.rst │ │ │ ├── MeanFilter.md │ │ │ ├── MaskDataFilter.md │ │ │ ├── NeighborhoodConnected.md │ │ │ ├── GaussianBlur.md │ │ │ ├── MedianFilter.md │ │ │ ├── OtsuThreshold.md │ │ │ └── ArithmeticFilter.md │ │ ├── MaskFilters │ │ │ ├── index.rst │ │ │ ├── BooleanOR.md │ │ │ ├── BooleanAND.md │ │ │ ├── BooleanRemove.md │ │ │ ├── BooleanXOR.md │ │ │ ├── FillHoles.md │ │ │ ├── ConnectedComponentSizeFilter.md │ │ │ └── ConnectedComponentsFilter.md │ │ ├── AdvancedFilters │ │ │ ├── index.rst │ │ │ ├── GradientMagnitude.md │ │ │ ├── DistanceMap.md │ │ │ ├── CurvatureAnisotropicDiffusion.md │ │ │ ├── GradientAnisotropicDiffusion.md │ │ │ ├── IntensityCorrection.md │ │ │ └── CannyEdge.md │ │ └── LargeVolumeTools │ │ │ ├── index.rst │ │ │ └── ExtractDataLayerTool.md │ └── Manuals │ │ ├── Functions │ │ ├── WelcomeScreen │ │ │ ├── Quit.md │ │ │ ├── OpenExistingProject.md │ │ │ ├── StartNewProject.md │ │ │ ├── LoadRecentProject.md │ │ │ ├── QuickOpenFile.md │ │ │ └── index.rst │ │ ├── Seg3DWindows │ │ │ ├── ControllerWindow │ │ │ │ ├── UndoRedoBuffer.md │ │ │ │ ├── EventLogTab.md │ │ │ │ ├── StateVariablesTab.md │ │ │ │ ├── index.rst │ │ │ │ └── ActionsTab.md │ │ │ ├── MessageHistoryWindow.md │ │ │ ├── VolumeViewWindow │ │ │ │ ├── index.rst │ │ │ │ ├── VolumeRenderingPanel.md │ │ │ │ ├── FogPanel.md │ │ │ │ └── TransferFunction.md │ │ │ ├── index.rst │ │ │ ├── ToolsWindow.md │ │ │ └── PythonConsole.md │ │ ├── BasicProgramFunctions │ │ │ ├── index.rst │ │ │ ├── Help.md │ │ │ └── Edit.md │ │ └── Seg3DViewer │ │ │ ├── index.rst │ │ │ ├── ViewerPanels │ │ │ └── index.rst │ │ │ └── ControllingWindows.md │ │ └── Seg3DBasicFunctionality_figures │ │ ├── Add.png │ │ ├── New.png │ │ ├── Close.png │ │ ├── Data.png │ │ ├── Mask.png │ │ ├── Minus.png │ │ ├── dock.png │ │ ├── AlignOff.png │ │ ├── ClipOff.png │ │ ├── FogOff.png │ │ ├── FogPanel.png │ │ ├── GridOff.png │ │ ├── InfoOff.png │ │ ├── LightOff.png │ │ ├── LockOff.png │ │ ├── Pref_gen.png │ │ ├── TextOff.png │ │ ├── WorldOff.png │ │ ├── layout.png │ │ ├── DownArrow.png │ │ ├── ExportSeg.png │ │ ├── OpacityOff.png │ │ ├── OverlayOff.png │ │ ├── PickingOff.png │ │ ├── Pref_side.png │ │ ├── Pref_view.png │ │ ├── RightArrow.png │ │ ├── SwitchTool.png │ │ ├── ToolWindow.png │ │ ├── VisibleOff.png │ │ ├── VolRendOpt.png │ │ ├── close_dock.png │ │ ├── newProject.png │ │ ├── quick_menu.png │ │ ├── AppearanceOff.png │ │ ├── AutoViewOff.png │ │ ├── ClippingPanel.png │ │ ├── DuplicateOff.png │ │ ├── ExportSeg_2.png │ │ ├── FlipHorizOff.png │ │ ├── FlipVertOff.png │ │ ├── ImportWidget.png │ │ ├── LayerOpacity.png │ │ ├── LayerWindow.png │ │ ├── Pref_layers.png │ │ ├── ProjectWindow.png │ │ ├── ProvenanceOff.png │ │ ├── Seg3D_layout.png │ │ ├── VolRendPanel.png │ │ ├── close_window.png │ │ ├── layout_blank.pdf │ │ ├── layout_blank.png │ │ ├── LayerAppearance.png │ │ ├── PickingLinesOff.png │ │ ├── geometric_info.png │ │ ├── welcome_screen.png │ │ ├── IsosurfaceMenuOff.png │ │ ├── PreviousSliceOff.png │ │ ├── ProvenanceWindow.png │ │ ├── SlicesVisibleOff.png │ │ ├── VolumeRenderingOff.png │ │ ├── VolumeVisibleOff.png │ │ ├── Controller_EventLog.png │ │ ├── Controller_OnStartup.png │ │ ├── Controller_OpenTool.png │ │ ├── IsosurfaceComputeOff.png │ │ ├── IsosurfaceDeleteOff.png │ │ ├── IsosurfaceVisibleOff.png │ │ ├── PythonConsole_blank.png │ │ ├── Controller_ActionList.png │ │ ├── Controller_UsabilityMsg.png │ │ ├── Controller_StateVariables.png │ │ ├── Controller_ToolStateVars.png │ │ └── InvisibleSlicesVisibleOff.png ├── tutorials │ └── Seg3DTutorial_figures │ │ ├── maskdata.png │ │ ├── AngioData.png │ │ ├── CannyAfter.png │ │ ├── CannyBefore.png │ │ ├── LoadVolume.png │ │ ├── OtsuAfter.png │ │ ├── OtsuBefore.png │ │ ├── Speedline.png │ │ ├── paintlumen.png │ │ ├── LoadVolume_2.png │ │ ├── MaskDataBrain.png │ │ ├── SpeedlineFill.png │ │ ├── polylinelumen.png │ │ ├── MainSeg3DWindow.png │ │ ├── MaskedPainting.png │ │ ├── Neighborhood_1.png │ │ ├── SpeedlineImage.png │ │ ├── ThresholdAngio.png │ │ ├── logicaloperators.png │ │ ├── welcome_screen.png │ │ ├── FilteredAngioData.png │ │ ├── KeyboardShortcuts.png │ │ ├── SkullSegmentation.png │ │ ├── creatingisosurface.png │ │ ├── LoadingBrainDataSet.png │ │ ├── LoadingSegmentation.png │ │ ├── Median-ImageCorrected.png │ │ ├── NeighborhoodConnected.png │ │ ├── ThresholdGreyMatter.png │ │ ├── ThresholdWHiteMatter.png │ │ ├── polylinesuperficial.png │ │ └── Cannywithmeanandlayers.png ├── _templates │ └── layout.html ├── requirements.txt ├── Makefile ├── make.bat └── references.bib ├── Superbuild ├── UseTetgen.cmake └── TetgenConfig.cmake.in ├── .gitmodules ├── .gitignore ├── scripts ├── README └── settings.ini ├── .travis.yml ├── README.md ├── .github └── workflows │ ├── linux.yml │ ├── mac.yml │ └── windows.yml └── .gitattributes /bin/.gitignore: -------------------------------------------------------------------------------- 1 | * 2 | -------------------------------------------------------------------------------- /src/Plugins/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /docs/_static/css/main.css: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /docs/bib.rst: -------------------------------------------------------------------------------- 1 | Bibliography 2 | ============ 3 | .. bibliography:: 4 | -------------------------------------------------------------------------------- /docs/_static/seg3d.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/_static/seg3d.png -------------------------------------------------------------------------------- /src/Resources/Icons/Seg3D.rc: -------------------------------------------------------------------------------- 1 | IDI_ICON1 ICON "seg3d2_32.ico" 2 | -------------------------------------------------------------------------------- /src/Resources/Icons/Seg3D.icns: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Icons/Seg3D.icns -------------------------------------------------------------------------------- /src/Resources/Images/Symbol.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Images/Symbol.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/hr.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/hr.png -------------------------------------------------------------------------------- /src/Resources/Footer_Icons/new.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Footer_Icons/new.png -------------------------------------------------------------------------------- /src/Resources/Icons/seg3d2_128.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Icons/seg3d2_128.ico -------------------------------------------------------------------------------- /src/Resources/Icons/seg3d2_128.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Icons/seg3d2_128.png -------------------------------------------------------------------------------- /src/Resources/Icons/seg3d2_16.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Icons/seg3d2_16.ico -------------------------------------------------------------------------------- /src/Resources/Icons/seg3d2_256.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Icons/seg3d2_256.ico -------------------------------------------------------------------------------- /src/Resources/Icons/seg3d2_256.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Icons/seg3d2_256.png -------------------------------------------------------------------------------- /src/Resources/Icons/seg3d2_32.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Icons/seg3d2_32.ico -------------------------------------------------------------------------------- /src/Resources/Icons/seg3d2_48.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Icons/seg3d2_48.ico -------------------------------------------------------------------------------- /src/Resources/Images/HelpWhite.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Images/HelpWhite.png -------------------------------------------------------------------------------- /src/ThirdParty/tinyxml/changes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/ThirdParty/tinyxml/changes.txt -------------------------------------------------------------------------------- /src/ThirdParty/tinyxml/tinystr.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/ThirdParty/tinyxml/tinystr.cpp -------------------------------------------------------------------------------- /src/Resources/General_Icons/exit.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/exit.png -------------------------------------------------------------------------------- /src/Resources/Images/Seg3DSplash.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Images/Seg3DSplash.png -------------------------------------------------------------------------------- /src/Resources/Images/VisibleGray.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Images/VisibleGray.png -------------------------------------------------------------------------------- /src/Resources/Images/VisibleOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Images/VisibleOff.png -------------------------------------------------------------------------------- /src/Resources/Images/VisibleWhite.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Images/VisibleWhite.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/CropGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/CropGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/MeanGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/MeanGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/PadGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/PadGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/body-bg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/body-bg.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/checker.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/checker.png -------------------------------------------------------------------------------- /src/Resources/Images/DownArrowWhite.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Images/DownArrowWhite.png -------------------------------------------------------------------------------- /src/Resources/Images/LabelMapWhite.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Images/LabelMapWhite.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/add_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/add_01.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/info_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/info_01.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/isoX_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/isoX_01.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/iso_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/iso_01.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/layers.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/layers.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/lock_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/lock_01.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/lock_03.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/lock_03.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/ISO_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/ISO_01.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/axisV.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/axisV.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/axisX.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/axisX.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/axisY.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/axisY.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/axisZ.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/axisZ.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/cut_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/cut_01.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/InvertGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/InvertGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/MeasureGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/MeasureGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/MedianGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/MedianGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/zip-icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/zip-icon.png -------------------------------------------------------------------------------- /src/Application/Tools/MeasurementTool.cc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Application/Tools/MeasurementTool.cc -------------------------------------------------------------------------------- /src/Resources/Footer_Icons/footer_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Footer_Icons/footer_01.png -------------------------------------------------------------------------------- /src/Resources/Footer_Icons/switch_tool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Footer_Icons/switch_tool.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress0.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress20.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress20.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress40.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress40.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress60.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress60.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress80.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress80.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/arrow-down.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/arrow-down.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/arrow-up.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/arrow-up.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/maximize.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/maximize.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/radio-fill.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/radio-fill.png -------------------------------------------------------------------------------- /src/Resources/Images/RightArrowWhite.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Images/RightArrowWhite.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/brush_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/brush_01.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/isoGo_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/isoGo_01.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/isoMenu_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/isoMenu_01.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/minus_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/minus_01.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/opacity_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/opacity_01.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/windowed.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/windowed.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/center_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/center_01.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/grid_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/grid_01.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/lock_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/lock_01.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/pick_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/pick_01.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/planes_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/planes_01.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/snap_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/snap_01.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/BooleanORGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/BooleanORGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/CannyEdgeGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/CannyEdgeGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/CopyPasteGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/CopyPasteGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/FillHolesGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/FillHolesGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/MaskDataGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/MaskDataGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/PolylineGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/PolylineGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/ResampleGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/ResampleGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/SpeedlineGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/SpeedlineGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/ThresholdGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/ThresholdGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/TransformGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/TransformGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/highlight-bg.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/highlight-bg.jpg -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/octocat-icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/octocat-icon.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/tar-gz-icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/tar-gz-icon.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress100.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress100.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress120.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress120.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress140.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress140.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress160.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress160.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress180.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress180.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress200.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress200.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress220.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress220.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress240.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress260.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress260.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress280.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress280.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress300.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress300.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress320.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress320.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/Progress340.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/Progress340.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/arrow-expand.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/arrow-expand.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/arrow-right.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/arrow-right.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/radio-empty.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/radio-empty.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/duplicate_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/duplicate_01.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/lighting_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/lighting_01.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/viewData_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/viewData_01.png -------------------------------------------------------------------------------- /Superbuild/UseTetgen.cmake: -------------------------------------------------------------------------------- 1 | include_directories(${TETGEN_INCLUDE}) 2 | add_definitions(-DTETLIBRARY) 3 | link_directories(${TETGEN_LIBRARY_DIR}) 4 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/ArithmeticGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/ArithmeticGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/BooleanANDGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/BooleanANDGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/BooleanXORGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/BooleanXORGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/DistanceMapGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/DistanceMapGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/FlipRotateGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/FlipRotateGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/GaussianBlurGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/GaussianBlurGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/PaintBrushGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/PaintBrushGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/SelectPointsGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/SelectPointsGUI.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/arrow-expanded.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/arrow-expanded.png -------------------------------------------------------------------------------- /src/Resources/Images/IsosurfaceVisibleGrey.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Images/IsosurfaceVisibleGrey.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/visibility_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/visibility_01.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/perspective_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/perspective_01.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/visibility_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/visibility_01.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/wireframe_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/wireframe_01.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/maskdata.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/maskdata.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/BooleanRemoveGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/BooleanRemoveGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/OtsuThresholdGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/OtsuThresholdGUI.png -------------------------------------------------------------------------------- /src/Documentation/presentations/Seg3DInsights.ppt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/presentations/Seg3DInsights.ppt -------------------------------------------------------------------------------- /src/Resources/General_Icons/checkbox-selected.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/checkbox-selected.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/color_transparent.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/color_transparent.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/mask_transparent.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/mask_transparent.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/visibilityPlus_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/visibilityPlus_01.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/flipVertical_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/flipVertical_01.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/AngioData.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/AngioData.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/CannyAfter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/CannyAfter.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/CannyBefore.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/CannyBefore.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/LoadVolume.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/LoadVolume.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/OtsuAfter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/OtsuAfter.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/OtsuBefore.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/OtsuBefore.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/Speedline.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/Speedline.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/paintlumen.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/paintlumen.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/ExtractDataLayersGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/ExtractDataLayersGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/PointSetRegisterGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/PointSetRegisterGUI.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/maskdata.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/maskdata.png -------------------------------------------------------------------------------- /src/Documentation/presentations/Seg3DVisInsights.ppt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/presentations/Seg3DVisInsights.ppt -------------------------------------------------------------------------------- /src/Resources/General_Icons/checkbox-unselected.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/checkbox-unselected.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/mask_bitplane_1248.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/mask_bitplane_1248.png -------------------------------------------------------------------------------- /src/Resources/Palette_Icons/mask_label_map_1234.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Palette_Icons/mask_label_map_1234.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/flipHorizontal_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/flipHorizontal_01.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/showSlicePlanes_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/showSlicePlanes_01.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/viewCrosshairs_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/viewCrosshairs_01.png -------------------------------------------------------------------------------- /src/Resources/Viewport_Icons/volumeRendering_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/Viewport_Icons/volumeRendering_01.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/LoadVolume_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/LoadVolume_2.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/MaskDataBrain.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/MaskDataBrain.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/SpeedlineFill.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/SpeedlineFill.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/polylinelumen.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/polylinelumen.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/Tools/index.rst: -------------------------------------------------------------------------------- 1 | Tools 2 | ======================================== 3 | 4 | .. toctree:: 5 | :maxdepth: 2 6 | :glob: 7 | 8 | * 9 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/ConfidenceConnectedGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/ConfidenceConnectedGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/ConnectedComponentGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/ConnectedComponentGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/IntensityCorrectionGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/IntensityCorrectionGUI.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/AngioData.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/AngioData.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/CannyAfter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/CannyAfter.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/LoadVolume.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/LoadVolume.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/OtsuAfter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/OtsuAfter.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/OtsuBefore.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/OtsuBefore.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/Speedline.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/Speedline.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/paintlumen.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/paintlumen.png -------------------------------------------------------------------------------- /src/Resources/General_Icons/checkbox-indeterminate.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Resources/General_Icons/checkbox-indeterminate.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/MainSeg3DWindow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/MainSeg3DWindow.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/MaskedPainting.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/MaskedPainting.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/Neighborhood_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/Neighborhood_1.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/SpeedlineImage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/SpeedlineImage.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/ThresholdAngio.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/ThresholdAngio.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/logicaloperators.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/logicaloperators.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/welcome_screen.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/welcome_screen.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/ConnectedComponentSizeGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/ConnectedComponentSizeGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/FastBinaryDilateErodeGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/FastBinaryDilateErodeGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/HistogramEqualizationGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/HistogramEqualizationGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/NeighborhoodConnectedGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/NeighborhoodConnectedGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/SegmentationLevelSetGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/SegmentationLevelSetGUI.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Add.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Add.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/New.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/New.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/CannyBefore.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/CannyBefore.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/LoadVolume_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/LoadVolume_2.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/MaskDataBrain.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/MaskDataBrain.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/SpeedlineFill.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/SpeedlineFill.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/polylinelumen.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/polylinelumen.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/FilteredAngioData.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/FilteredAngioData.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/KeyboardShortcuts.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/KeyboardShortcuts.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/SkullSegmentation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/SkullSegmentation.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/creatingisosurface.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/creatingisosurface.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/WelcomeScreen/Quit.md: -------------------------------------------------------------------------------- 1 | # Quit 2 | 3 | This option will quit Seg3D. This exists for the rare occasion that you accidentally open Seg3D. 4 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/SmoothBinaryDilateErodeGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/SmoothBinaryDilateErodeGUI.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Close.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Close.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Data.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Data.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Mask.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Mask.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Minus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Minus.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/dock.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/dock.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/MainSeg3DWindow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/MainSeg3DWindow.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/MaskedPainting.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/MaskedPainting.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/Neighborhood_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/Neighborhood_1.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/SpeedlineImage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/SpeedlineImage.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/ThresholdAngio.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/ThresholdAngio.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/welcome_screen.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/welcome_screen.png -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- 1 | [submodule "src/ThirdParty/submodules/googletest"] 2 | path = src/ThirdParty/submodules/googletest 3 | url = https://github.com/CIBC-Internal/googletest.git 4 | -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/LoadingBrainDataSet.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/LoadingBrainDataSet.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/LoadingSegmentation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/LoadingSegmentation.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/Median-ImageCorrected.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/Median-ImageCorrected.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/NeighborhoodConnected.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/NeighborhoodConnected.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/ThresholdGreyMatter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/ThresholdGreyMatter.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/ThresholdWHiteMatter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/ThresholdWHiteMatter.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/polylinesuperficial.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/polylinesuperficial.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Add.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Add.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/New.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/New.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/DataFilters/index.rst: -------------------------------------------------------------------------------- 1 | Data Filters 2 | ======================================== 3 | 4 | .. toctree:: 5 | :maxdepth: 2 6 | :glob: 7 | 8 | * 9 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/MaskFilters/index.rst: -------------------------------------------------------------------------------- 1 | Mask Filters 2 | ======================================== 3 | 4 | .. toctree:: 5 | :maxdepth: 2 6 | :glob: 7 | 8 | * 9 | -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/AlignOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/AlignOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/ClipOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/ClipOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/FogOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/FogOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/FogPanel.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/FogPanel.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/GridOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/GridOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/InfoOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/InfoOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/LightOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/LightOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/LockOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/LockOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Pref_gen.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Pref_gen.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/TextOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/TextOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/WorldOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/WorldOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/layout.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/layout.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/FilteredAngioData.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/FilteredAngioData.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/KeyboardShortcuts.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/KeyboardShortcuts.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/SkullSegmentation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/SkullSegmentation.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/creatingisosurface.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/creatingisosurface.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/logicaloperators.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/logicaloperators.png -------------------------------------------------------------------------------- /docs/tutorials/Seg3DTutorial_figures/Cannywithmeanandlayers.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/tutorials/Seg3DTutorial_figures/Cannywithmeanandlayers.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Close.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Close.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Data.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Data.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Mask.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Mask.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Minus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Minus.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/dock.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/dock.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/AdvancedFilters/index.rst: -------------------------------------------------------------------------------- 1 | Advanced Filters 2 | ======================================== 3 | 4 | .. toctree:: 5 | :maxdepth: 2 6 | :glob: 7 | 8 | * 9 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/CurvatureAnisotropicDiffusionGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/CurvatureAnisotropicDiffusionGUI.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/images/GradientAnisotropicDiffusionGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Tools/images/GradientAnisotropicDiffusionGUI.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/DownArrow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/DownArrow.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/ExportSeg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/ExportSeg.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/OpacityOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/OpacityOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/OverlayOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/OverlayOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/PickingOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/PickingOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Pref_side.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Pref_side.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Pref_view.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Pref_view.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/RightArrow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/RightArrow.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/SwitchTool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/SwitchTool.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/ToolWindow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/ToolWindow.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/VisibleOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/VisibleOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/VolRendOpt.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/VolRendOpt.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/close_dock.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/close_dock.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/newProject.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/newProject.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/quick_menu.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/quick_menu.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/LoadingBrainDataSet.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/LoadingBrainDataSet.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/LoadingSegmentation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/LoadingSegmentation.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/ThresholdGreyMatter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/ThresholdGreyMatter.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/ThresholdWHiteMatter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/ThresholdWHiteMatter.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/polylinesuperficial.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/polylinesuperficial.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/AlignOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/AlignOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ClipOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ClipOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/FogOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/FogOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/FogPanel.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/FogPanel.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/GridOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/GridOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/InfoOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/InfoOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/LightOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/LightOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/LockOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/LockOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Pref_gen.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Pref_gen.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/TextOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/TextOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/WorldOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/WorldOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/layout.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/layout.png -------------------------------------------------------------------------------- /docs/user_docs/Tools/LargeVolumeTools/index.rst: -------------------------------------------------------------------------------- 1 | Large Volume Tools 2 | ======================================== 3 | 4 | .. toctree:: 5 | :maxdepth: 2 6 | :glob: 7 | 8 | * 9 | -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/AppearanceOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/AppearanceOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/AutoViewOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/AutoViewOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/ClippingPanel.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/ClippingPanel.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/DuplicateOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/DuplicateOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/ExportSeg_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/ExportSeg_2.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/FlipHorizOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/FlipHorizOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/FlipVertOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/FlipVertOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/ImportWidget.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/ImportWidget.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/LayerOpacity.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/LayerOpacity.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/LayerWindow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/LayerWindow.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Pref_layers.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Pref_layers.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/ProjectWindow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/ProjectWindow.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/ProvenanceOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/ProvenanceOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Seg3D_layout.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Seg3D_layout.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/VolRendPanel.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/VolRendPanel.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/close_window.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/close_window.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/layout_blank.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/layout_blank.pdf -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/layout_blank.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/layout_blank.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/Cannywithmeanandlayers.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/Cannywithmeanandlayers.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/Median-ImageCorrected.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/Median-ImageCorrected.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DTutorial_figures/NeighborhoodConnected.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DTutorial_figures/NeighborhoodConnected.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/DownArrow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/DownArrow.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ExportSeg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ExportSeg.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/OpacityOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/OpacityOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/OverlayOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/OverlayOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/PickingOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/PickingOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Pref_side.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Pref_side.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Pref_view.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Pref_view.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/RightArrow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/RightArrow.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/SwitchTool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/SwitchTool.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ToolWindow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ToolWindow.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/VisibleOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/VisibleOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/VolRendOpt.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/VolRendOpt.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/close_dock.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/close_dock.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/newProject.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/newProject.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/quick_menu.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/quick_menu.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/LayerAppearance.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/LayerAppearance.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/PickingLinesOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/PickingLinesOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/geometric_info.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/geometric_info.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/welcome_screen.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/welcome_screen.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/AppearanceOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/AppearanceOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/AutoViewOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/AutoViewOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ClippingPanel.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ClippingPanel.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/DuplicateOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/DuplicateOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ExportSeg_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ExportSeg_2.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/FlipHorizOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/FlipHorizOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/FlipVertOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/FlipVertOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ImportWidget.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ImportWidget.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/LayerOpacity.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/LayerOpacity.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/LayerWindow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/LayerWindow.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Pref_layers.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Pref_layers.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ProjectWindow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ProjectWindow.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ProvenanceOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ProvenanceOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Seg3D_layout.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Seg3D_layout.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/VolRendPanel.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/VolRendPanel.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/close_window.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/close_window.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/layout_blank.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/layout_blank.pdf -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/layout_blank.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/layout_blank.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/IsosurfaceMenuOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/IsosurfaceMenuOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/PreviousSliceOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/PreviousSliceOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/ProvenanceWindow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/ProvenanceWindow.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/SlicesVisibleOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/SlicesVisibleOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/VolumeRenderingOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/VolumeRenderingOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/VolumeVisibleOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/VolumeVisibleOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/LayerAppearance.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/LayerAppearance.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/PickingLinesOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/PickingLinesOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/geometric_info.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/geometric_info.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/welcome_screen.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/welcome_screen.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Controller_EventLog.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Controller_EventLog.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Controller_OnStartup.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Controller_OnStartup.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Controller_OpenTool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Controller_OpenTool.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/IsosurfaceComputeOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/IsosurfaceComputeOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/IsosurfaceDeleteOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/IsosurfaceDeleteOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/IsosurfaceVisibleOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/IsosurfaceVisibleOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/PythonConsole_blank.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/PythonConsole_blank.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/IsosurfaceMenuOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/IsosurfaceMenuOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/PreviousSliceOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/PreviousSliceOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ProvenanceWindow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/ProvenanceWindow.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/SlicesVisibleOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/SlicesVisibleOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/VolumeRenderingOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/VolumeRenderingOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/VolumeVisibleOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/VolumeVisibleOff.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Controller_ActionList.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Controller_ActionList.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Controller_UsabilityMsg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Controller_UsabilityMsg.png -------------------------------------------------------------------------------- /Superbuild/TetgenConfig.cmake.in: -------------------------------------------------------------------------------- 1 | set(TETGEN_INCLUDE "@TETGEN_INCLUDE@") 2 | set(TETGEN_LIBRARY_DIR "@TETGEN_LIBRARY_DIR@") 3 | set(TETGEN_LIBRARY "@TETGEN_LIBRARY@") 4 | set(TETGEN_USE_FILE "@TETGEN_USE_FILE@") -------------------------------------------------------------------------------- /docs/_templates/layout.html: -------------------------------------------------------------------------------- 1 | {% extends "!layout.html" %} 2 | {% block rootrellink %} 3 |
  • Project Homepage »
    • 4 | {{ super() }} 5 | {% endblock %} 6 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Controller_EventLog.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Controller_EventLog.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Controller_OnStartup.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Controller_OnStartup.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Controller_OpenTool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Controller_OpenTool.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/IsosurfaceComputeOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/IsosurfaceComputeOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/IsosurfaceDeleteOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/IsosurfaceDeleteOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/IsosurfaceVisibleOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/IsosurfaceVisibleOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/PythonConsole_blank.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/PythonConsole_blank.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Controller_StateVariables.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Controller_StateVariables.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/Controller_ToolStateVars.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/Controller_ToolStateVars.png -------------------------------------------------------------------------------- /src/Documentation/Seg3DBasicFunctionality_figures/InvisibleSlicesVisibleOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/src/Documentation/Seg3DBasicFunctionality_figures/InvisibleSlicesVisibleOff.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Controller_ActionList.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Controller_ActionList.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Controller_UsabilityMsg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Controller_UsabilityMsg.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Controller_StateVariables.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Controller_StateVariables.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Controller_ToolStateVars.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/Controller_ToolStateVars.png -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/InvisibleSlicesVisibleOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SCIInstitute/Seg3D/HEAD/docs/user_docs/Manuals/Seg3DBasicFunctionality_figures/InvisibleSlicesVisibleOff.png -------------------------------------------------------------------------------- /src/Application/Renderer/OrientationArrowsShader.frag: -------------------------------------------------------------------------------- 1 | // GLSL fragment shader for rendering the orientation arrows 2 | 3 | vec4 compute_lighting(); 4 | 5 | void main() 6 | { 7 | gl_FragColor = gl_Color * compute_lighting(); 8 | } 9 | -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- 1 | docutils 2 | pygments 3 | linkify-it-py 4 | lxml 5 | myst-parser 6 | sphinx 7 | sphinx-issues 8 | sphinx-markdown-tables 9 | sphinx-notfound-page 10 | furo 11 | sphinxcontrib-bibtex 12 | sphinx-markdown-tables 13 | -------------------------------------------------------------------------------- /src/Application/Renderer/OrientationArrowsShader.vert: -------------------------------------------------------------------------------- 1 | // GLSL vertex shader for rendering the orientation arrows 2 | 3 | void compute_lighting(); 4 | 5 | void main() 6 | { 7 | compute_lighting(); 8 | 9 | gl_FrontColor = gl_Color; 10 | gl_BackColor = gl_Color; 11 | 12 | gl_Position = ftransform(); 13 | } 14 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/WelcomeScreen/OpenExistingProject.md: -------------------------------------------------------------------------------- 1 | # Open Existing Project 2 | 3 | This option is the same as the **File** ⇒ **[Open Project](../BasicProgramFunctions/File.md#open-project)** menu item. It will open a dialogue window to allow the user to choose an existing *\*.s3d* or *\*.seg3dproj* file to load into Seg3D. 4 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/Seg3DWindows/ControllerWindow/UndoRedoBuffer.md: -------------------------------------------------------------------------------- 1 | # Undo/Redo Buffer 2 | 3 | The Undo/Redo Buffer stores past actions for the current open project. Closing the session will erase the buffers. In these buffers a user can find the actions, in order, than can be either undone or redone by using Seg3D’s Undo and Redo options. 4 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *.pdb 2 | *.ilk 3 | *.exe 4 | *.idb 5 | *.swp 6 | *.vcxproj* 7 | *DS_Store 8 | bin* 9 | *.dylib 10 | *.so 11 | *.a 12 | *.*~ 13 | CMakeCache.txt 14 | CMakeFiles 15 | src/Makefile 16 | cmake_install.cmake 17 | install_manifest.txt 18 | CTestTestfile.cmake 19 | DartConfiguration.tcl 20 | xCode_bin* 21 | 22 | # Sphinx builds 23 | docs/_build/ 24 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/MaskFilters/BooleanOR.md: -------------------------------------------------------------------------------- 1 | # Boolean OR 2 | 3 | The Boolean OR filter produces the union of two masks. 4 | 5 | ## Detailed Description 6 | 7 | The Boolean OR filter will input two mask layers and output the union of the two masks, i.e., the pixels that are masked by either of the two input masks. 8 | 9 | ![alt text](../images/BooleanORGUI.png) 10 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/WelcomeScreen/StartNewProject.md: -------------------------------------------------------------------------------- 1 | # Start New Project 2 | 3 | This option is the same as the **File** ⇒ **[New Project](../BasicProgramFunctions/File.md#new-project)** menu item. It will display the New Project Wizard ({numref}`fig-new-project`), allowing the user to choose a project name and location so that the project can be saved easily and automatically. 4 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/MaskFilters/BooleanAND.md: -------------------------------------------------------------------------------- 1 | # Boolean AND 2 | 3 | The Boolean AND filter finds the intersection of two masks. 4 | 5 | ## Detailed Description 6 | 7 | The Boolean AND filter will input two mask layers and output the intersection of the two masks, i.e., the pixels that are masked by both of the two input masks. 8 | 9 | ![alt text](../images/BooleanANDGUI.png) 10 | -------------------------------------------------------------------------------- /src/CMake/ReadMe.txt: -------------------------------------------------------------------------------- 1 | DESCRIPTION 2 | =========== 3 | 4 | Seg3D is a light weight program for segmenting biomedical volumetric data. The program contains a series of tools for manipulating images and for creating label masks, that describe structures of interest. The program allows for both manual segmentation as well as semi-manual segmentation where the user is aided by automated filters. 5 | -------------------------------------------------------------------------------- /src/Configuration/ActionPythonWrapperFunctionSource.in: -------------------------------------------------------------------------------- 1 | static boost::python::object action_@ACTION@_python_wrapper( 2 | boost::python::tuple args, boost::python::dict kw_args ) 3 | { 4 | boost::python::list arg_list( args ); 5 | arg_list.insert( 0, "@ACTION@" ); 6 | boost::python::tuple complete_args( arg_list ); 7 | return Core::RunActionFromPython( complete_args, kw_args ); 8 | } 9 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/BasicProgramFunctions/index.rst: -------------------------------------------------------------------------------- 1 | Basic Program Functions 2 | ======================================== 3 | 4 | This section gives a brief overview of the options found under the File, Edit, and Help menus. These menus contain options that allow you to save and open new projects, and set preferences. 5 | 6 | .. toctree:: 7 | :maxdepth: 2 8 | :glob: 9 | 10 | * 11 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/BasicProgramFunctions/Help.md: -------------------------------------------------------------------------------- 1 | # Help 2 | 3 | This menu provides additional information on other features and modules. It has two basic functions: 4 | 5 | ## Search 6 | 7 | This feature allows you to search all the menus by typing in a search box. 8 | 9 | ## Keyboard Shortcuts 10 | 11 | This function opens a list of all the keyboard and mouse shortcuts available in Seg3D. 12 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/Tools/SelectPointsTool.md: -------------------------------------------------------------------------------- 1 | # Select Points 2 | 3 | Select and export a set of points. 4 | 5 | ## Detailed Description 6 | 7 | This tool selects a set of points either in pixel or actual (world) coordinates and save as a text file. It works with either data or mask layers. Clicking on a layer in one of the 2D views places a point. Secondary (*right mouse* button) click deletes a point. 8 | 9 | ![alt text](../images/SelectPointsGUI.png) 10 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/WelcomeScreen/LoadRecentProject.md: -------------------------------------------------------------------------------- 1 | # Load Recent Project 2 | 3 | This option allows the users to quickly open a project recently opened in Seg3D. The list of recent projects is shown in the text box above the **Load Recent Project** button. This option will be unavailable unless one of the recent projects in the list is selected. Updating or reinstalling Seg3D may erase the saved list of recent projects even though the projects still exist. 4 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/MaskFilters/BooleanRemove.md: -------------------------------------------------------------------------------- 1 | # Boolean Remove 2 | 3 | The Boolean REMOVE filter removes the intersecting region of two masks from the first. 4 | 5 | ## Detailed Description 6 | 7 | The Boolean REMOVE filter will input two mask layers and use the second input to remove the intersecting regions from the first. The result of this can be thought of as the first region minus the second region. 8 | 9 | ![alt text](../images/BooleanRemoveGUI.png) 10 | -------------------------------------------------------------------------------- /src/BuildNotes.txt: -------------------------------------------------------------------------------- 1 | Seg3D Image Registrations tools build notes: 2 | 3 | Windows: 4 | - building FFTW as an ITK CMake external is NOT supported on Windows 5 | - tried downloading precompiled library zip file from fftw website, 3.3.4 64-bit release 6 | - enable ITK_USE_SYSTEM_FFTW 7 | - set FFTW_INCLUDE_PATH=c:/fftw-3.3.4-dll64, 8 | FFTWD_LIB=c:/fftw-3.3.4-dll64/libfftw3-3.dll (not sure this is correct), 9 | FFTWF_LIB=c:/fftw-3.3.4-dll64/libfftw3f-3.dll 10 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/Seg3DWindows/MessageHistoryWindow.md: -------------------------------------------------------------------------------- 1 | # Message History Window 2 | 3 | The Message History Window is not opened by default when Seg3D is opened. This window is opened by clicking on the message history icon in the bottom left of the screen in the [tool bar](../Seg3DViewer/ToolBar.md) ({numref}`table-tool-bottom-icons`). This window will show the messages that Seg3D displays when many functions are performed. This can be used to track your steps at a high level. 4 | -------------------------------------------------------------------------------- /src/CMake/Welcome.txt: -------------------------------------------------------------------------------- 1 | Welcome to the Seg3D installation. 2 | 3 | This program will guide you through the process of installing Seg3D on your computer. 4 | 5 | Seg3D is a light weight program for segmenting biomedical volumetric data. The program contains a series of tools for manipulating images and for creating label masks, that describe structures of interest. The program allows for both manual segmentation as well as semi-manual segmentation where the user is aided by automated filters. 6 | 7 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/MaskFilters/BooleanXOR.md: -------------------------------------------------------------------------------- 1 | # Boolean XOR 2 | 3 | This filter produces the unique regions of two masks. 4 | 5 | ## Detailed Description 6 | 7 | The Boolean XOR filter will input two mask layers and output the unique union regions of the two masks, i.e., the pixels that are masked by exactly one of the two input masks. This filter is the same as removing the result of the Boolean AND filter from the result of the Boolean OR filter. 8 | 9 | ![alt text](../images/BooleanXORGUI.png) 10 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/Tools/InvertTool.md: -------------------------------------------------------------------------------- 1 | # Invert 2 | 3 | This tool will make a negative of the input data. 4 | 5 | ## Detailed Description 6 | 7 | This tool will invert the data in a layer to its minimum and maximum, making a negative of the input data. If performed on a mask layer, this tool will be a mask of everything in the volume besides the original mask. If performed on image data, the intensities will be reversed so that the dark areas look light and vis versa. 8 | 9 | ![alt text](../images/InvertGUI.png) 10 | -------------------------------------------------------------------------------- /src/Application/Renderer/Fog.vert: -------------------------------------------------------------------------------- 1 | // GLSL vertex shader for per-fragment fog computation 2 | 3 | uniform vec2 fog_range; 4 | // Fog depth in eye space. 5 | // This is a workaround for Macs with ATI X1600/X1900. 6 | // On those cards accessing gl_FragCoord would cause fallback to software renderer. 7 | varying float fog_depth; 8 | 9 | void compute_fog_depth() 10 | { 11 | vec4 eye_coord_pos = gl_ModelViewMatrix * gl_Vertex; 12 | fog_depth = ( -eye_coord_pos.z - fog_range[ 0 ] ) / ( fog_range[ 1 ] - fog_range[ 0 ] ); 13 | } 14 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/Tools/PadTool.md: -------------------------------------------------------------------------------- 1 | # Pad 2 | 3 | The Pad tool allows the user to pad one or more volumes. This tool can be used on both mask and data layers. 4 | 5 | ## Detailed Description 6 | 7 | The Pad amount is set manually using the sliders. There are options to resample with the same ratio in every direction (check *Constrain Aspect* option) or to resample each direction independently (must uncheck *Constrain Aspect* option to enable). Pad values can be zero, the dataset min or max. 8 | 9 | ![alt text](../images/PadGUI.png) 10 | -------------------------------------------------------------------------------- /src/Application/Renderer/Fog.frag: -------------------------------------------------------------------------------- 1 | // GLSL fragment shader for per-fragment fog computation 2 | 3 | // Fog depth in eye space. 4 | // This is a workaround for Macs with ATI X1600/X1900. 5 | // On those cards accessing gl_FragCoord would cause fallback to software renderer. 6 | varying float fog_depth; 7 | 8 | float compute_fog_factor() 9 | { 10 | float z = fog_depth; 11 | float fog_factor = exp( -gl_Fog.density * gl_Fog.density * z * z ); 12 | fog_factor = clamp( fog_factor, 0.0, 1.0 ); 13 | 14 | return fog_factor; 15 | } 16 | -------------------------------------------------------------------------------- /scripts/README: -------------------------------------------------------------------------------- 1 | This directory contains some sample/test scripts for the registration tools recently added to Seg3D. The configuration file settings.in contains file paths used on a test computer. 2 | 3 | Scripts: 4 | MV_basic_pipeline1.py: tests MouseVolume dataset registration using fft, stos brute and slice to volume filters. 5 | polson3319_pipeline1.py: tests Polson3319 dataset registration using fft, refine grid, stos brute and slice to volume filters. Uses tiling hints, currently. 6 | stitch.py: tests aagam's heart data set using tiling hints. 7 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/Seg3DWindows/ControllerWindow/EventLogTab.md: -------------------------------------------------------------------------------- 1 | # Event Log Tab 2 | 3 | The event log shows actions that have been taken on the session since the latest load of the session. If Seg3D is closed, and then reopened, the event log will only record the history for the newly opened session. This differs from the action tab in this way, which collects actions for the entire history of the session. The event log also differs from the action log in that it records all events involved with running Seg3D, not just the actions. This is also a non-editable tab. 4 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/WelcomeScreen/QuickOpenFile.md: -------------------------------------------------------------------------------- 1 | # Quick Open File 2 | 3 | This option is the same as the **File** ⇒ **[Import Layer From Single File...](../BasicProgramFunctions/File.md#import-layer-from-single-file)** menu item. You may choose a file to load into Seg3D for viewing. All of the filters and tools will be available, but the project can not be saved automatically until a project name is created by using the **File** ⇒ **[Save Project As](../BasicProgramFunctions/File.md#save-project-as)** menu item. 4 | This option does not allow the opening of image stacks. 5 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | os: linux 2 | dist: bionic 3 | 4 | compiler: 5 | - gcc 6 | - clang 7 | before_install: 8 | - sudo apt-get -qq --yes update 9 | # packages for headless build 10 | - sudo apt-get -qq --yes install ninja-build mesa-common-dev libgl1-mesa-dev libglu1-mesa-dev mesa-utils-extra libglapi-mesa libglapi-mesa qt5-qmake qtbase5-dev libqt5opengl5-dev libqt5svg5-dev 11 | script: 12 | - cd bin 13 | - cmake -GNinja -DTRAVIS_BUILD:BOOL=ON -DQt5_PATH=$(dpkg -L qtbase5-dev) ../Superbuild 14 | - travis_wait 70 ninja 15 | 16 | after_success: 17 | - cd Seg3D 18 | - ninja test 19 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/DataFilters/MeanFilter.md: -------------------------------------------------------------------------------- 1 | # Mean 2 | 3 | This filter performs smoothing on the data layer using a step function. 4 | 5 | ## Detailed Description 6 | 7 | The Mean filter performs a smoothing on the data layer using a discrete step function kernel. For every pixel (except the edges), this filter performs an averaging of the neighboring pixels. This filter will reduce noise by averaging it out, but will also reduce edges. The neighborhood size is controlled by the distance parameter, the greater the distance, the more smoothing. 8 | 9 | ![alt text](../images/MeanGUI.png) 10 | -------------------------------------------------------------------------------- /src/Application/Renderer/SliceShader.vert: -------------------------------------------------------------------------------- 1 | // GLSL vertex shader for rendering a slice 2 | 3 | uniform bool enable_lighting; 4 | uniform bool enable_fog; 5 | 6 | void compute_lighting(); 7 | void compute_fog_depth(); 8 | 9 | void main() 10 | { 11 | if ( enable_lighting ) 12 | { 13 | compute_lighting(); 14 | } 15 | 16 | gl_TexCoord[0] = gl_MultiTexCoord0; 17 | gl_TexCoord[1] = gl_MultiTexCoord1; 18 | #ifndef DISABLE_CLIPPING 19 | gl_ClipVertex = gl_ModelViewMatrix * gl_Vertex; 20 | #endif 21 | gl_Position = ftransform(); 22 | 23 | if ( enable_fog ) 24 | { 25 | compute_fog_depth(); 26 | } 27 | } 28 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/Seg3DWindows/ControllerWindow/StateVariablesTab.md: -------------------------------------------------------------------------------- 1 | # State Variables Tab 2 | 3 | The state variables tab shows a list of all the state settings for the session. Settings cannot be edited in this window, instead use the built-in get and set functions . The state variables include Seg3D viewer settings, tool and filter arguments and settings. For example, {numref}`fig-tool-state-vars` shows Threshold tool state variables. 4 | 5 | :::{figure-md} fig-tool-state-vars 6 | 7 | ![ToolStateVars](../../../Seg3DBasicFunctionality_figures/Controller_ToolStateVars.png) 8 | 9 | Threshold tool state variables. 10 | ::: 11 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/AdvancedFilters/GradientMagnitude.md: -------------------------------------------------------------------------------- 1 | # Gradient Magnitude 2 | 3 | This filter calculates the Gradient magnitude of a data layer and output in a data layer. 4 | 5 | ## Detailed Description 6 | 7 | The Gradient Magnitude filter will calculate the Gradient Magnitude of a data layer and output a new or replaced data layer containing the Gradient Magnitude. The Gradient Magnitude is useful as it can highlight regions with edges in the data image because those regions have high gradients. 8 | 9 | This filter is very simple to use because there is only one input and no parameters to adjust, so choose a data layer and go. 10 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | [Seg3D](http://www.seg3d.org) is a free volume segmentation and processing tool developed by the NIH Center for Integrative Biomedical Computing at the University of Utah Scientific Computing and Imaging (SCI) Institute. Seg3D combines a flexible manual segmentation interface with powerful higher-dimensional image processing and segmentation algorithms from the Insight Toolkit. Users can explore and label image volumes using volume rendering and orthogonal slice view windows. 2 | 3 | Seg3D [build instructions and documentation](http://sciinstitute.github.io/seg3d.pages). 4 | 5 | [![Build Status](https://travis-ci.org/SCIInstitute/Seg3D.svg?branch=master)](https://travis-ci.org/SCIInstitute/Seg3D) 6 | -------------------------------------------------------------------------------- /src/Main/Seg3DLib/Seg3DLib_example_main.cc: -------------------------------------------------------------------------------- 1 | #include 2 | #include 3 | #include "Lib/Seg3D_lib.h" 4 | 5 | void showSeg3DWidget() 6 | { 7 | Seg3DLibrary::makeSeg3DWidget()->show(); 8 | } 9 | 10 | int main(int argc, char *argv[]) 11 | { 12 | QApplication app(argc, argv); 13 | auto Context = Seg3DLibrary::Context::makeContext(&app); 14 | 15 | // dummy application code 16 | QPushButton runSeg3DasWidget("Click to run Seg3D as a widget"); 17 | runSeg3DasWidget.resize(200, 30); 18 | QObject::connect(&runSeg3DasWidget, &QPushButton::clicked, showSeg3DWidget); 19 | runSeg3DasWidget.show(); 20 | // end dummy application 21 | 22 | return app.exec(); 23 | } 24 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/Tools/FlipRotateTool.md: -------------------------------------------------------------------------------- 1 | # Flip/Rotate 2 | 3 | This tool will flip or rotate one or more layers around an axis. 4 | 5 | ## Detailed Description 6 | 7 | The Flip/Rotate tool will flip or rotate 90 degrees one or more layers around a specified axis. This tool will flip/rotate multiple layers from the same group to the same size by choosing them in the list of layers near the top of the window. After choosing the desired layers to flip/rotate, the action is performed when the button for that action is pressed. There are three flipping options (flipping each axis) and six rotation option (clockwise and counter-clockwise in each plane). 8 | 9 | ![alt text](../images/FlipRotateGUI.png) 10 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line, and also 5 | # from the environment for the first two. 6 | SPHINXOPTS ?= 7 | SPHINXBUILD ?= sphinx-build 8 | SOURCEDIR = . 9 | BUILDDIR = _build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 21 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/Seg3DWindows/VolumeViewWindow/index.rst: -------------------------------------------------------------------------------- 1 | Volume View Window 2 | ======================================== 3 | 4 | The Volume View Window is not opened by default when Seg3D is opened. To open the window, click the ’Window’ option in the task bar and select the Volume View option. The window may also be toggled by using the key command: Shift+CTRL/CMD+V. Once activated, the window will appear on the right and side of the Seg3D panel covering the layer mask window. To toggle back to the layer mask window, click the Layer Manager tab at the bottom of the page. The Volume View Window has three separate options for volume displaying. 5 | 6 | .. toctree:: 7 | :maxdepth: 2 8 | :glob: 9 | 10 | * 11 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/Seg3DWindows/index.rst: -------------------------------------------------------------------------------- 1 | Seg3D Windows 2 | ======================================== 3 | 4 | In addition to the viewer windows discussed in the above chapter, there are several other windows involved in streamlining the user interface of the Seg3D software. Each of these windows can be accessed through the ’Window’ drop-down menu. By default these windows appear in certain positions defined below, but each can be undocked from the Seg3D interface and either left as stand alone windows or repositioned elsewhere on the Seg3D application (see :doc:`Controlling Windows <../Seg3DViewer/ControllingWindows>`). 5 | 6 | .. toctree:: 7 | :maxdepth: 2 8 | :glob: 9 | 10 | ControllerWindow/index 11 | VolumeViewWindow/index 12 | * 13 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/LargeVolumeTools/ExtractDataLayerTool.md: -------------------------------------------------------------------------------- 1 | # Extract Data Layers 2 | 3 | Select one of the levels of detail from the large data volume and convert it into a normal data layer. 4 | 5 | ## Detailed Description 6 | 7 | Once a volume is converted, the user can run any filter on the data. Currently, data layers should not have more than 4096 pixels in a single dimension, as data layers are not rendered as bricks, but as a single texture. 8 | 9 | It is expected that the ExtractDataLayer and Crop tools will often be used together, with a user cropping a region of the large volume and then selecting an appropriate level of resolution to convert the large volume layer into a normal data layer. 10 | 11 | ![alt text](../images/ExtractDataLayersGUI.png) 12 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/AdvancedFilters/DistanceMap.md: -------------------------------------------------------------------------------- 1 | # Distance Map 2 | 3 | This filter will calculate the distance to the surface of the mask from within the volume. 4 | 5 | ## Detailed Description 6 | 7 | The Distance Map filter will calculate the distance to the surface of a mask for every pixel in the volume. This filter will output a distance map as a data layer with the values considered inside the mask marked as negative. This filter is useful in many applications, such as providing an indicator function for the surface of the mask. This distance map can also be used to generated a smoother isosurface than may be possible from the original segmentation. The user may choose between pixel distance or actual distance. 8 | 9 | ![alt text](../images/DistanceMapGUI.png) 10 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/DataFilters/MaskDataFilter.md: -------------------------------------------------------------------------------- 1 | # Mask Data 2 | 3 | This filter will use a mask layer to discard data in the data layer. 4 | 5 | ## Detailed Description 6 | 7 | The Mask Data filter will use the second input of a mask layer to selectively discard (retain) data in a data layer. The pixels in the data layer that correspond to marked pixels in the mask layer will be kept, and the remaining pixels will be discarded by setting them to some background value. The background value can be set to zero, the original max or min value, or the new max or min value. This can be useful in isolating regions of interest and will eliminate noise from outside the region. This filter could also cause artificial edges to occur. 8 | 9 | ![alt text](../images/MaskDataGUI.png) 10 | -------------------------------------------------------------------------------- /src/Main/Seg3DLib/Lib/Seg3D_lib.h: -------------------------------------------------------------------------------- 1 | #ifndef SEG3D_LIB_H__ 2 | #define SEG3D_LIB_H__ 3 | 4 | #include 5 | #include 6 | 7 | class QWidget; 8 | class QApplication; 9 | 10 | namespace Seg3DLibrary 11 | { 12 | class ContextImpl; 13 | 14 | class Context 15 | { 16 | public: 17 | ~Context(); 18 | static std::unique_ptr makeContext(QApplication* app); 19 | 20 | private: 21 | ContextImpl* impl_; 22 | explicit Context(QApplication* app); 23 | Context(const Context&); 24 | Context& operator=(const Context&); 25 | }; 26 | 27 | QWidget* makeSeg3DWidget(); 28 | void importDataFile(const QString& data_filename); 29 | void importSegFile(const QString& seg_filename); 30 | void exportSegFile(const QString& export_path); 31 | } 32 | #endif 33 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/Seg3DWindows/ControllerWindow/index.rst: -------------------------------------------------------------------------------- 1 | Controller Window 2 | ======================================== 3 | The Controller Window is not opened by default when Seg3D is opened. To open the window, click the ’Window’ option in the task bar and select the Controller option. The window may also be toggled by using the key command: Shift+CTRL/CMD+C. Notice the Controller Window option in the window drop-down menu is located below a separator. This indicates that the window will open a new pop-up window outside of the general Seg3D user interface. 4 | 5 | The Controller window supplies the user with all of the data, variables, history, and logs of the current Seg3D session. There are four tabs that can be selected in this window: 6 | 7 | .. toctree:: 8 | :maxdepth: 2 9 | :glob: 10 | 11 | * 12 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/DataFilters/NeighborhoodConnected.md: -------------------------------------------------------------------------------- 1 | # Neighborhood Connected 2 | 3 | This filter creates a mask indicating pixels within a value range and connected to seed points. 4 | 5 | ## Detailed Description 6 | 7 | The Neighborhood Connected filter is like a combination of the Threshold tool and the Connected Component filter. The user places seed points in the volume using the 2D viewers (**left mouse** to place, **right mouse** to remove). Then the filter will create a mask layer marking the pixels that are within the data value range of the seed locations that are also connected to the seed points. This tools is useful in segmenting long and winding structures as long as there is sufficient contrast between the desired structure and the surrounding medium. 8 | 9 | ![alt text](../images/NeighborhoodConnectedGUI.png) 10 | -------------------------------------------------------------------------------- /src/Application/Renderer/IsosurfaceShader.frag: -------------------------------------------------------------------------------- 1 | // GLSL fragment shader for rendering an isosurface 2 | 3 | uniform bool enable_lighting; 4 | uniform bool use_colormap; 5 | uniform sampler1D colormap; 6 | varying float normalized_value; 7 | uniform bool enable_fog; 8 | uniform float opacity; 9 | 10 | vec4 compute_lighting(); 11 | float compute_fog_factor(); 12 | 13 | void main() 14 | { 15 | vec4 color; 16 | if ( use_colormap ) 17 | { 18 | color = texture1D( colormap, normalized_value ); 19 | } 20 | else 21 | { 22 | color = gl_Color; 23 | } 24 | 25 | color.a = opacity; 26 | 27 | if ( enable_lighting ) 28 | { 29 | color.rgb = ( color * compute_lighting() ).rgb; 30 | } 31 | 32 | if ( enable_fog ) 33 | { 34 | color = mix( gl_Fog.color, color, compute_fog_factor() ); 35 | } 36 | 37 | gl_FragColor = color; 38 | } 39 | -------------------------------------------------------------------------------- /.github/workflows/linux.yml: -------------------------------------------------------------------------------- 1 | name: linux-build 2 | 3 | on: [push, pull_request] 4 | 5 | jobs: 6 | linux-build-gui: 7 | 8 | runs-on: ${{ matrix.os }} 9 | strategy: 10 | matrix: 11 | os: [ubuntu-18.04, ubuntu-latest] 12 | 13 | steps: 14 | - name: Checkout 15 | uses: actions/checkout@v2 16 | 17 | - name: Prepare 18 | run: sudo apt-get update && sudo apt-get install mesa-common-dev libgl1-mesa-dev mesa-utils-extra libglapi-mesa ninja-build qt5-qmake qtbase5-dev libqt5opengl5-dev libqt5svg5-dev 19 | 20 | - name: Install Qt 21 | uses: jurplel/install-qt-action@v2 22 | with: 23 | version: 5.14.2 24 | target: desktop 25 | host: linux 26 | install-deps: true 27 | 28 | - name: Build 29 | run: ./build.sh -DQt5_PATH="${Qt5_Dir}" -j3 30 | continue-on-error: true 31 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/DataFilters/GaussianBlur.md: -------------------------------------------------------------------------------- 1 | # Gaussian Blur 2 | 3 | This filter performs a smoothing on the data layer. 4 | 5 | ## Detailed Description 6 | 7 | The Gaussian Blur filter performs a smoothing on the data layer using a discrete Gaussian kernel. For every pixel (except the edges), this filter performs a weighted averaging of the neighboring pixels where the weights are a 3D Gaussian distribution centered at the pixel. This filter will reduce noise by averaging it out, but will also reduce edges. 8 | 9 | The *distance* parameter set with the slider bar in the tool window determines the size of the neighborhood so that the bigger the distance, the greater the area of averaging and thus more blurring. Since the *distance* parameter is the only exposed parameter, the variance is dependent on the distance. 10 | 11 | ![alt text](../images/GaussianBlurGUI.png) 12 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/MaskFilters/FillHoles.md: -------------------------------------------------------------------------------- 1 | # Fill Holes 2 | 3 | This filter can be used to fill unmarked regions in a mask layer. 4 | 5 | ## Detailed Description 6 | 7 | The Fill Holes filter can be used to fill unmarked regions which are surrounded by a data in a mask layer. This is useful when automated segmentation techniques leave false negative noise, or regions that should have been marked but aren't. This filter will only fill regions that are completely surrounded with mask data. Therefore, if the filter appears to not work at filter, check the holes and make sure they are not exposed to the background. The seed points can be used to if there is a hole that is on the edge, but the hole must not be the majority of the edge, i.e. the background. In this case the seeds are used to identify the background. Seed points are not needed otherwise. 8 | 9 | ![alt text](../images/FillHolesGUI.png) 10 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/DataFilters/MedianFilter.md: -------------------------------------------------------------------------------- 1 | # Median 2 | 3 | This is a nonlinear filter for reducing noise but maintaining edges. 4 | 5 | ## Detailed Description 6 | 7 | The Median filter is a non-linear filter that will reduce noise (speckle), but may also preserve or enhance sharp boundaries. For every pixel (except the edges), this filter finds the median value of the neighboring pixels and uses this value to replace the original pixel. This causes the edges to be preserved, if the neighborhood is appropriately sized, while eliminating subtle variations. 8 | 9 | The neighborhood is controlled by the *distance* parameter. Though increasing the distance will also increase the smoothing, it is because the size requirement for regions to not be eliminated. Clear divisions of large regions will increase in contrast and smaller regions will be smoothed out. 10 | 11 | ![alt text](../images/MedianGUI.png) 12 | -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | pushd %~dp0 4 | 5 | REM Command file for Sphinx documentation 6 | 7 | if "%SPHINXBUILD%" == "" ( 8 | set SPHINXBUILD=sphinx-build 9 | ) 10 | set SOURCEDIR=. 11 | set BUILDDIR=_build 12 | 13 | if "%1" == "" goto help 14 | 15 | %SPHINXBUILD% >NUL 2>NUL 16 | if errorlevel 9009 ( 17 | echo. 18 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx 19 | echo.installed, then set the SPHINXBUILD environment variable to point 20 | echo.to the full path of the 'sphinx-build' executable. Alternatively you 21 | echo.may add the Sphinx directory to PATH. 22 | echo. 23 | echo.If you don't have Sphinx installed, grab it from 24 | echo.http://sphinx-doc.org/ 25 | exit /b 1 26 | ) 27 | 28 | %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 29 | goto end 30 | 31 | :help 32 | %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 33 | 34 | :end 35 | popd 36 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/WelcomeScreen/index.rst: -------------------------------------------------------------------------------- 1 | Welcome Screen 2 | ======================================== 3 | 4 | Anytime you start Seg3D, users are first presented with the Seg3D welcome screen. As seen below, the welcome screen consists of the Seg3D splash screen and a menu displaying the available options for starting and continuing a segmentation in Seg3D. The included options are to load a recent project, open existing project, start a new project, quickly open a file for viewing, and to quit Seg3D. These options are the same as some of the options in the **File** menu which are explained in this chapter as well as the :doc:`File <../BasicProgramFunctions/File>` page. 5 | 6 | .. figure:: ../../Seg3DBasicFunctionality_figures/welcome_screen.png 7 | :width: 495 px 8 | :align: center 9 | 10 | Seg3D welcome screen. 11 | 12 | 13 | .. toctree:: 14 | :maxdepth: 2 15 | :glob: 16 | 17 | * 18 | -------------------------------------------------------------------------------- /src/Application/Renderer/IsosurfaceShader.vert: -------------------------------------------------------------------------------- 1 | // GLSL vertex shader for rendering an isosurface 2 | 3 | uniform bool enable_lighting; 4 | uniform bool enable_fog; 5 | uniform bool use_colormap; 6 | uniform float min_val; 7 | uniform float val_range; 8 | attribute float value; 9 | varying float normalized_value; 10 | 11 | void compute_lighting(); 12 | void compute_fog_depth(); 13 | 14 | void main() 15 | { 16 | if ( enable_lighting ) 17 | { 18 | compute_lighting(); 19 | } 20 | 21 | if ( enable_fog ) 22 | { 23 | compute_fog_depth(); 24 | } 25 | 26 | gl_TexCoord[0] = gl_MultiTexCoord0; 27 | gl_TexCoord[1] = gl_MultiTexCoord1; 28 | gl_FrontColor = gl_Color; 29 | gl_BackColor = gl_Color; 30 | if ( use_colormap ) 31 | { 32 | normalized_value = ( value - min_val ) / val_range; 33 | } 34 | #ifndef DISABLE_CLIPPING 35 | gl_ClipVertex = gl_ModelViewMatrix * gl_Vertex; 36 | #endif 37 | gl_Position = ftransform(); 38 | } 39 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | # Based on https://help.github.com/articles/dealing-with-line-endings/ 2 | # Set the default behavior, in case people don't have core.autocrlf set. 3 | * text=auto 4 | 5 | # Explicitly declare text files you want to always be normalized and converted 6 | # to native line endings on checkout. 7 | *.c text 8 | *.cc text 9 | *.cxx text 10 | *.cpp text 11 | *.h text 12 | *.hxx text 13 | *.hpp text 14 | *.cmake text 15 | *.txt text 16 | *.qrc text 17 | 18 | # Declare files that will always have CRLF line endings on checkout. 19 | *.sln text eol=crlf 20 | *.cbproj eol=crlf 21 | *.vcproj eol=crlf 22 | *.groupproj eol=crlf 23 | *.vsprops eol=crlf 24 | *.props eol=crlf 25 | *.qc eol=crlf 26 | *.rc eol=crlf 27 | 28 | # Declare files that will always have LF line endings on checkout. 29 | *.plist eol=lf 30 | 31 | # Denote all files that are truly binary and should not be modified. 32 | *.png binary 33 | *.jpg binary 34 | *.ico binary 35 | *.icns binary 36 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/MaskFilters/ConnectedComponentSizeFilter.md: -------------------------------------------------------------------------------- 1 | # Connected Component Size 2 | 3 | Similar to the Connected Component filter, this filter will return a image data layer but the data value will correspond to its size (logarithmic or linear scale). 4 | 5 | ## Detailed Description 6 | 7 | The Connected Component Size filter is similar to the Connected Component Filter, but will return a image data layer labeling each connected region with a data value corresponding to its size (logarithmic or linear scale). This allows the user to manipulate the connected regions in the volume based on size. For example, thresholding real data can yield several regions of interest that are correct maskings of the data, but may also capture small regions of noise in other areas of the scan. These small regions of noise can be eliminated using the Connected Component filter by using the Threshold tool on the result. 8 | 9 | ![alt text](../images/ConnectedComponentSizeGUI.png) 10 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/Seg3DWindows/VolumeViewWindow/VolumeRenderingPanel.md: -------------------------------------------------------------------------------- 1 | # Volume Rendering Panel 2 | 3 | :::{figure-md} fig-vol-rend-panel 4 | 5 | ![VolRendPanel](../../../Seg3DBasicFunctionality_figures/VolRendPanel.png) 6 | 7 | Volume View Window - Volume Rendering Panel Displayed. Show volume rendering icon at the bottom of the viewer window must be activated. 8 | ::: 9 | 10 | The volume rendering panel allows users to generate a volume directly from the volume file, based on the application of transfer functions. These volume representations are created by extracting values from the transfer functions available and displaying them on a slice-by-slice basis. If the user zooms the image in closely, each individual slice can be seen ({numref}`fig-vol-rend-opt`). The user must define the volume over which they would like to perform the volume rendering. The user must also make sure that the ’show volume rendering’ option is selected at the bottom of the 3D viewer window. 11 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/Seg3DWindows/VolumeViewWindow/FogPanel.md: -------------------------------------------------------------------------------- 1 | # Fog Panel 2 | 3 | The Fog Panel allows the user to control the fog density. In order to observe the effects of fog, the user must activate the Show fog icon on the bottom of the 3D viewer window. Once active, a fog will be observed on the image. The depth of the fog is determined by the distance that the 3-dimensional component is away from the viewer. In {numref}`fig-fog-panel`, the pelvis is tilted away from the viewer. It is therefore farther from the viewer and has more fog effect applied to it. 4 | 5 | Fog density can be tuned by using the slider in the the Volume View Window. By default the density value is 1.00. If the fog density increases, the fogging effect increases. 6 | 7 | :::{figure-md} fig-fog-panel 8 | 9 | ![FogPanel](../../../Seg3DBasicFunctionality_figures/FogPanel.png) 10 | 11 | Volume View Window - Fog Panel Displayed. The user must activate the Show fog option at the bottom of the viewer window. 12 | ::: 13 | -------------------------------------------------------------------------------- /src/CMake/Scripts/build_full_static_lib.bat.in: -------------------------------------------------------------------------------- 1 | SET all_libs_dest_dir=@ALL_LIBS_DEST_DIR@ 2 | SET superbuild_dir=@SUPERBUILD_LIBS_SOURCE_DIR_CMD@ 3 | SET zlib_file=@ZLIB_FILE@ 4 | SET vs_bin_path=@_vs_bin_path@ 5 | SET dependencies_dest_dir=@DEPENDENCIES_DEST_DIR@ 6 | SET batch_file_path=@BATCH_FILE_PATH@ 7 | SET lib_tool_path=@LIB_TOOL_PATH@ 8 | 9 | rmdir /S /Q %all_libs_dest_dir% 10 | mkdir %all_libs_dest_dir% 11 | 12 | cd %superbuild_dir% 13 | for /r %%A IN (*.lib) DO copy %%A %all_libs_dest_dir% 14 | copy %zlib_file% %all_libs_dest_dir% 15 | del %all_libs_dest_dir%\Seg3D_lib.lib 16 | del %all_libs_dest_dir%\Seg3D_dependencies.lib 17 | del %all_libs_dest_dir%\Seg3D_lib_complete.lib 18 | 19 | del %dependencies_dest_dir%\Seg3D_dependencies.lib 20 | del %dependencies_dest_dir%\Seg3D_lib_complete.lib 21 | %batch_file_path% & %lib_tool_path% /OUT:%dependencies_dest_dir%\Seg3D_dependencies.lib %all_libs_dest_dir%\*.lib & %lib_tool_path% /OUT:%dependencies_dest_dir%\Seg3D_lib_complete.lib %dependencies_dest_dir%\*.lib 22 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/MaskFilters/ConnectedComponentsFilter.md: -------------------------------------------------------------------------------- 1 | # Connected Component 2 | 3 | This filter finds connected data regions in a mask layer that are coincident to the defined seed points. 4 | 5 | ## Detailed Description 6 | 7 | The Connected Component filter finds connected data regions in a mask layer that are coincident to the defined seed points. This filter can be used to eliminate mask data that is not connected (separated by a blank pixel) from a desired region and can thus reduce noise in the segmentation. 8 | 9 | The seed points are chosen by **left clicking** in the 2D viewers or deleted by **right clicking** on existing seed points. Multiple connected regions can be selected with these seed points. Another mask can be used as a seed. Using a mask layer second input field will cause the filter to find regions from the first input that are overlapping or next to any data in the second input. Additional seed points can be used or ignored with the use seed points option. 10 | 11 | ![alt text](../images/ConnectedComponentGUI.png) 12 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/Seg3DWindows/ToolsWindow.md: -------------------------------------------------------------------------------- 1 | # Tools Window 2 | 3 | The tools window is another of the three windows that is opened upon Seg3D launch. This window is also on the left of the Seg3D panel and is, unlike the project window, is displayed when Seg3D is opened. Users can toggle between project and tool windows by selecting the specific tabs at the bottom of the left most window pane. 4 | 5 | The tool window houses the current tools that the user has selected from the ’Tools’ drop down menu. The active tool will be highlighted in orange and will be displayed. Inactive tools, that have been opened during the session, will be grayed out and minimized. To access one of the other tools, click one of the grayed out items or select it from the ’Tools’ drop down menu. In {numref}`fig-tool-window`, the ’Paint Brush’ tool is active, while the ’Threshold,’ ’Crop,’ and ’Measure’ tools are inactive. 6 | 7 | :::{figure-md} fig-tool-window 8 | 9 | ![ToolWindow](../../Seg3DBasicFunctionality_figures/ToolWindow.png) 10 | 11 | Tools Window 12 | ::: 13 | -------------------------------------------------------------------------------- /src/CMake/Modules/CPack.Distribution.dist.in: -------------------------------------------------------------------------------- 1 | 2 | 3 | @CPACK_PACKAGE_NAME@ 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | @CPACK_PACKAGE_NAME@.pkg 21 | 22 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/DataFilters/OtsuThreshold.md: -------------------------------------------------------------------------------- 1 | # Otsu Threshold 2 | 3 | This filter creates a mask of regions data clusters. 4 | 5 | ## Detailed Description 6 | 7 | The Otsu Threshold filter attempts to cluster data values in a data layer based upon how similar they are and create mask layers identifying the regions of similar data. This filter provides a good quick segmentation in many cases. There is a [Wikipedia article](http://en.wikipedia.org/wiki/Otsu%27s_method) containing a good description of the Otsu threshold algorithm. 8 | 9 | Using the Ostu Threshold filter is simple. The only parameter in this implementation is the number of thresholds (1 to 4), or the number of divisions in the volume. The results of this filter are mutually exclusive (no output will mask the same pixel as another layer) and collectively exhaustive (the whole volume will be mask by one of the output layers) so that there will be one more mask layer generated than thresholds used. A histogram is presented to aid the user in choosing the threshold number. 10 | 11 | ![alt text](../images/OtsuThresholdGUI.png) 12 | -------------------------------------------------------------------------------- /scripts/settings.ini: -------------------------------------------------------------------------------- 1 | [MouseVolume] 2 | dir=/Volumes/scratch/seg3d2_irtools/TestData/MouseVolume 3 | image_ext=.tif 4 | shrink=8 5 | spacing=1.0 6 | first_slice=1 7 | last_slice=18 8 | overlap_min=0.04 9 | overlap_max=0.22 10 | 11 | [test] 12 | dir=/home/sci/brig/Downloads/testmultiple1 13 | number_prefix=slice_ 14 | image_ext=.png 15 | shrink=4 16 | spacing=1.0 17 | first_slice=5 18 | last_slice=525 19 | overlap_min=0.05 20 | overlap_max=0.22 21 | clahe_window_dim=2 22 | clahe_shrink=2 23 | pyramid_iters=50 24 | pyramid_levels=2 25 | min_peak=0.2 26 | peak_threshold=0.2 27 | tile_strategy=top_left_book 28 | 29 | [Polson3319] 30 | dir=/usr/sci/projects/msmg/data/Polson3319slices 31 | outputDir=/Volumes/scratch/seg3d2_irtools/Polson3319 32 | mosaic_ext=.mosaic 33 | image_ext=.tif 34 | stos_ext=.stos 35 | shrink=8 36 | first_slice=39 37 | last_slice=247 38 | overlap_min=0.1 39 | overlap_max=0.22 40 | spacing=1.0 41 | pyramid_iters=50 42 | clahe_window_dim=128 43 | clahe_shrink=1 44 | assemble_feathering_option=blend 45 | volume_shrink=0 46 | pyramid_levels=2 47 | min_peak=0.2 48 | peak_threshold=0.1 49 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/AdvancedFilters/CurvatureAnisotropicDiffusion.md: -------------------------------------------------------------------------------- 1 | # Curvature Anisotropic Diffusion 2 | 3 | This filter performs anisotropic diffusion using the modified curvature diffusion equation (MCDE). 4 | 5 | ## Detailed Description 6 | 7 | The Curvature Anisotropic Diffusion performs anisotropic diffusion on a data layer using the modified curvature diffusion equation (MCDE). Anisotropic diffusion filtering is used to reduce noise (or unwanted detail) in images while preserving specific image features, such as edges and is based on the work of Pietro Perona and Jalhandra Malik, {cite:p}`PM1990`. The output of this filter is a smoothed data layer. 8 | 9 | The parameters for this filter are *Iterations* and *Sensitivity Range.* The *iterations* parameter will control how many iterations of the filter will be executed. The more iterations, the smoother the image. The *sensitivity range* parameter controls the 'diffusion' of the objects in the image, therefore the higher the sensitivity, the more 'diffusion' and thus more smoothing. 10 | 11 | ![alt text](../images/CurvatureAnisotropicDiffusionGUI.png) 12 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/AdvancedFilters/GradientAnisotropicDiffusion.md: -------------------------------------------------------------------------------- 1 | # Gradient Anisotropic Diffusion 2 | 3 | This filter performs anisotropic diffusion on a data layer and an additional edge enhancing step. 4 | 5 | ## Detailed Description 6 | 7 | The Gradient Anisotropic Diffusion performs anisotropic diffusion on a data layer and uses an additional edge enhancing step to preserve useful features. Anisotropic diffusion filtering is used to reduce noise (or unwanted detail) in images while preserving specific image features, such as edges and is based on the work of Pietro Perona and Jalhandra Malik, {cite:p}`PM1990`. The output of this filter is a smoothed data layer. 8 | 9 | The parameters for this filter are *Iterations* and *Sensitivity Range*. The *Iterations* parameter will control how many iterations of the filter will be executed. The more iterations, the smoother the image. The *sensitivity range* parameter controls the 'diffusion' of the objects in the image, therefore the higher the sensitivity, the more 'diffusion' and thus more smoothing. 10 | 11 | ![alt text](../images/GradientAnisotropicDiffusionGUI.png) 12 | -------------------------------------------------------------------------------- /src/CMake/Scripts/repair_package.sh.in: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | seg3dbuild_dir=@CMAKE_BINARY_DIR@ 4 | productbuild_dir=@PKG_BUILD_DIR@ 5 | productroot_dir=@PKG_ROOT_DIR@ 6 | 7 | if [[ ! -e $productroot_dir ]]; then 8 | echo "$productroot_dir does not exist" 9 | exit 1 10 | fi 11 | 12 | @PKGBUILD_EXE@ --analyze --root $productroot_dir $seg3dbuild_dir/@CPACK_PACKAGE_NAME@.plist 13 | @PKGBUILD_EXE@ --identifier edu.utah.sci.@CPACK_PACKAGE_NAME@ --root $productroot_dir \ 14 | --component-plist $seg3dbuild_dir/@CPACK_PACKAGE_NAME@.plist \ 15 | --install-location /Applications $seg3dbuild_dir/@CPACK_PACKAGE_NAME@.pkg 16 | @PRODUCTBUILD_EXE@ --distribution $seg3dbuild_dir/CPack.Distribution.dist \ 17 | --package-path $productroot_dir $productbuild_dir/tmp.pkg 18 | # Tip: pkgutil --expand can be used to debug package building 19 | @PKGUTIL_EXE@ --expand $productbuild_dir/tmp.pkg $productbuild_dir/tmp 20 | @PKGUTIL_EXE@ --flatten $productbuild_dir/tmp $seg3dbuild_dir/@PKG_FILE_NAME@.pkg 21 | rm -f $seg3dbuild_dir/@CPACK_PACKAGE_NAME@.pkg $seg3dbuild_dir/@CPACK_PACKAGE_NAME@.plist 22 | rm -Rf $productbuild_dir/tmp 23 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/Seg3DViewer/index.rst: -------------------------------------------------------------------------------- 1 | Seg3D Viewer 2 | ======================================== 3 | 4 | The Seg3D viewer is the main interface between the users and the software. This viewer is meant to be highly interactive and intuitive. Using a combination of mouse functions, keyboard shortcuts, and visual buttons the users can quickly visualize and segment data. This chapter will describe the functionality of several aspects of the Seg3D viewer including the overall layout of the interface, 2D slice viewer, 3D volume viewer, and the various viewing options available. 5 | 6 | .. figure:: ../../Seg3DBasicFunctionality_figures/layout_blank.pdf 7 | :width: 495 px 8 | :align: center 9 | 10 | Seg3D interface. 11 | 12 | The default layout when Seg3D is opened and a new project is created is shown in the figure above. As seen from the image the interface for Seg3D consists of a number of viewers (both 2D and 3D), windows to control the functionality of Seg3D, and a tool bar at the bottom of the screen. 13 | 14 | .. toctree:: 15 | :maxdepth: 2 16 | :glob: 17 | 18 | ViewerPanels/index 19 | * 20 | -------------------------------------------------------------------------------- /.github/workflows/mac.yml: -------------------------------------------------------------------------------- 1 | name: mac-build 2 | 3 | on: [push, pull_request] 4 | 5 | jobs: 6 | mac-build-gui: 7 | 8 | runs-on: macOS-latest 9 | 10 | steps: 11 | - name: Checkout 12 | uses: actions/checkout@v2 13 | 14 | - name: Install Qt 15 | uses: jurplel/install-qt-action@v2 16 | with: 17 | version: 5.14.2 18 | target: desktop 19 | host: mac 20 | install-deps: true 21 | 22 | - name: Prepare 23 | run: | 24 | ln -s /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers/X11/ /usr/local/include/X11 25 | 26 | - name: make 27 | run: ./build.sh -DQt5_PATH="${Qt5_Dir}" 28 | 29 | - name: Package 30 | working-directory: bin/Seg3D 31 | run: | 32 | make package 33 | chmod +x repair_package.sh 34 | ./repair_package.sh 35 | 36 | - name: Upload installer 37 | uses: actions/upload-artifact@v2 38 | with: 39 | name: Seg3DMacInstaller 40 | path: bin/Seg3D/Seg3D2-2.*-Darwin.pkg 41 | -------------------------------------------------------------------------------- /src/Application/Renderer/Lighting.vert: -------------------------------------------------------------------------------- 1 | // GLSL vertex shader for headlight shading 2 | 3 | varying vec4 diffuse, ambient_global, ambient; // Light components. 4 | varying vec3 light_dir; // Light direction 5 | varying vec3 half_vector; // Half vector between eye and light source. 6 | // In the case of head light, it's the same as eye vector. 7 | varying float dist; // Distance to light source. 8 | varying vec3 normal; // The normal vector. 9 | 10 | void compute_lighting() 11 | { 12 | vec4 eye_coord_pos; // The position of the vertex in eye space 13 | vec3 aux; 14 | 15 | normal = normalize( gl_NormalMatrix * gl_Normal ); 16 | 17 | eye_coord_pos = gl_ModelViewMatrix * gl_Vertex; 18 | 19 | // With headlight, light position is alway at the origin in eye space 20 | aux = vec3( -eye_coord_pos ); 21 | light_dir = normalize( aux ); 22 | dist = length(aux); 23 | 24 | half_vector = light_dir; 25 | 26 | diffuse = gl_FrontMaterial.diffuse * gl_LightSource[0].diffuse; 27 | ambient = gl_FrontMaterial.ambient * gl_LightSource[0].ambient; 28 | ambient_global = gl_LightModel.ambient * gl_FrontMaterial.ambient; 29 | } 30 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/Seg3DWindows/PythonConsole.md: -------------------------------------------------------------------------------- 1 | # Python Console 2 | 3 | The Python Console window is not opened by default when Seg3D is opened. To open the window, click the ’Window’ option in the task bar and select the Python option. The window may also be toggled by using the key command: Shift+CTRL/CMD+Y. Notice the Python Window option in the window drop-down menu is located below a separator. This indicates that the window will open a new pop-up window outside of the general Seg3D user interface. 4 | 5 | The Python Window opens a Python scripting console that can be used by advanced users to control Seg3D ({numref}`fig-python-console`). Python code wrappers are generated allowing tools, filters, the viewer and data to be controlled in Python scripts. Basic Seg3D Python code samples are available under [Python Code Snippets](../../../../py_docs/python). An extensive treatment of python coding will not be attempted in this document; for more information on python coding, consult other resources. 6 | 7 | :::{figure-md} fig-python-console 8 | 9 | ![PythonConsole](../../Seg3DBasicFunctionality_figures/PythonConsole_blank.png) 10 | 11 | Python Console Window 12 | ::: 13 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/BasicProgramFunctions/Edit.md: -------------------------------------------------------------------------------- 1 | # Edit 2 | 3 | The Edit menu contains several features which are convenient for working on a project. 4 | 5 | ## Undo 6 | 7 | This function allows the user to undo a changes made to the unsaved project. Changes made to the project are stored in a buffer, the size of which can be changed under Seg3D preferences. This function can be called using the shortcut CTRL/CMD+Z. 8 | 9 | ## Redo 10 | 11 | Redo an operation on a project that was previously undone. This function can be called using the shortcut Shift+CTRL/CMD+Z. 12 | 13 | ## Copy Mask Slice 14 | 15 | Copy a single slice from a mask layer which can then be pasted onto other layers. This function can be called using the shortcut CTRL/CMD+C. 16 | 17 | ## Paste Mask Slice 18 | 19 | Paste a previously copied label from one slice of a mask label to all the slices of another mask label. This function can be called using the shortcut CTRL/CMD+V. 20 | 21 | ## Punch Through Volume 22 | 23 | After creating new label data on a single slice of a mask layer, that label can be copied or “punched” to every other slice by selecting this option. This function can be called using the shortcut CTRL/CMD+P. 24 | -------------------------------------------------------------------------------- /src/Application/Renderer/Lighting.frag: -------------------------------------------------------------------------------- 1 | // GLSL fragment shader for headlight shading 2 | 3 | varying vec4 diffuse, ambient_global, ambient; // Light components. 4 | varying vec3 light_dir; // Light direction 5 | varying vec3 half_vector; // Half vector between eye and light source. 6 | // In the case of head light, it's the same as eye vector. 7 | varying float dist; // Distance to light source. 8 | varying vec3 normal; // The normal vector. 9 | 10 | vec4 compute_lighting() 11 | { 12 | vec3 n, half_v; 13 | float n_dot_l, n_dot_hv; 14 | vec4 color = ambient_global; 15 | 16 | n = normalize( normal ); 17 | vec3 light_dir_norm = normalize( light_dir ); 18 | n_dot_l = dot ( n, light_dir_norm ); 19 | 20 | if ( n_dot_l < 0.0 ) 21 | { 22 | n_dot_l = -n_dot_l; 23 | n = -n; 24 | } 25 | 26 | if ( n_dot_l > 0.0 ) 27 | { 28 | color += ( diffuse * n_dot_l + ambient ); 29 | 30 | half_v = normalize(half_vector); 31 | n_dot_hv = max( dot ( n, half_v ), 0.0 ); 32 | color += gl_FrontMaterial.specular * gl_LightSource[0].specular * 33 | pow( n_dot_hv, gl_FrontMaterial.shininess ); 34 | } 35 | 36 | return color; 37 | } 38 | -------------------------------------------------------------------------------- /src/CMake/License.txt: -------------------------------------------------------------------------------- 1 | For more information, please see: http://software.sci.utah.edu 2 | 3 | The MIT License 4 | 5 | Copyright (c) 2017 Scientific Computing and Imaging Institute, University of Utah. 6 | 7 | 8 | Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: 9 | 10 | The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. 11 | 12 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 13 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/Seg3DViewer/ViewerPanels/index.rst: -------------------------------------------------------------------------------- 1 | Viewer Panels 2 | ======================================== 3 | 4 | .. figure:: ../../../Seg3DBasicFunctionality_figures/layout_blank.pdf 5 | :width: 495 px 6 | :align: center 7 | 8 | Seg3D interface. 9 | 10 | As seen in the screenshot above, there are a number of viewer panels in Seg3D, though the exact number can be set (see :doc:`Viewing Options <../ViewingOptions>`. Each of these viewer windows can be changed in size and in type. The type options are: volume, axial, sagittal, and coronal. The names of the 2D planes can be changed by the user in :doc:`Preferences <../../BasicProgramFunctions/Preferences>`. You can change the view of each pane by clicking on the view name and choosing the view to change it too. This is a drop down menu, so you can scroll over the name and the view will also change. There are also shortcuts to change views (V–Volume, X–Sagittal, Y–Coronal, and Z–Axial). There are several icons in each view panel, as well as mouse and keyboard shortcuts. The controls for each of the 2D viewers will be described below, as will the controls for the 3D volume viewer. 11 | 12 | .. toctree:: 13 | :maxdepth: 2 14 | :glob: 15 | :caption: Contents: 16 | 17 | * 18 | -------------------------------------------------------------------------------- /src/License.txt: -------------------------------------------------------------------------------- 1 | For more information, please see: http://software.sci.utah.edu 2 | 3 | The MIT License 4 | 5 | Copyright (c) 2017 Scientific Computing and Imaging Institute, 6 | University of Utah. 7 | 8 | Permission is hereby granted, free of charge, to any person obtaining a 9 | copy of this software and associated documentation files (the "Software"), 10 | to deal in the Software without restriction, including without limitation 11 | the rights to use, copy, modify, merge, publish, distribute, sublicense, 12 | and/or sell copies of the Software, and to permit persons to whom the 13 | Software is furnished to do so, subject to the following conditions: 14 | 15 | The above copyright notice and this permission notice shall be included 16 | in all copies or substantial portions of the Software. 17 | 18 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 19 | OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 20 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 21 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 22 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 23 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 24 | DEALINGS IN THE SOFTWARE. 25 | -------------------------------------------------------------------------------- /src/Core/VolumeRenderer/VolumeShaderOcclusion.vert: -------------------------------------------------------------------------------- 1 | // GLSL vertex shader for slice based volume rendering 2 | 3 | uniform vec3 tex_bbox_min; // Minimum values of texture position in world space 4 | uniform vec3 tex_bbox_size; // Size of texture in world space 5 | 6 | varying vec2 correction_factor; 7 | varying vec4 clip_space_pos; 8 | 9 | // Vertex position in world coordinates 10 | varying vec4 world_coord_pos; 11 | 12 | // Half vector between eye and light source. 13 | varying vec3 half_vector; 14 | // The light direction is always in +Z in eye space 15 | const vec3 light_dir = vec3( 0.0, 0.0, 1.0 ); 16 | 17 | void main() 18 | { 19 | // The position of the vertex in eye space 20 | vec4 eye_coord_pos = gl_ModelViewMatrix * gl_Vertex; 21 | 22 | vec3 eye_vec = vec3( -eye_coord_pos ); 23 | eye_vec = normalize( eye_vec ); 24 | half_vector = normalize( ( eye_vec + light_dir ) * 0.5 ); 25 | 26 | vec4 proj_scale = gl_ProjectionMatrix * vec4( 1.0, 1.0, eye_coord_pos.z, 1.0 ); 27 | correction_factor = proj_scale.xy / proj_scale.w; 28 | 29 | world_coord_pos = gl_Vertex; 30 | gl_TexCoord[0].stp = (gl_Vertex.xyz - tex_bbox_min)/tex_bbox_size; 31 | gl_ClipVertex = gl_ModelViewMatrix * gl_Vertex; 32 | clip_space_pos = ftransform(); 33 | gl_Position = clip_space_pos; 34 | } 35 | -------------------------------------------------------------------------------- /.github/workflows/windows.yml: -------------------------------------------------------------------------------- 1 | name: windows-build 2 | 3 | on: [push, pull_request] 4 | 5 | jobs: 6 | 7 | windows-build-gui: 8 | strategy: 9 | matrix: 10 | qtversion: [5.12.8, 5.14.2] 11 | runs-on: windows-2016 12 | 13 | steps: 14 | 15 | - name: Checkout 16 | uses: actions/checkout@v2 17 | 18 | - name: Install Qt 19 | uses: jurplel/install-qt-action@v2 20 | with: 21 | version: ${{ matrix.qtversion }} 22 | target: desktop 23 | host: windows 24 | arch: win64_msvc2017_64 25 | install-deps: true 26 | 27 | - name: Configure 28 | working-directory: bin 29 | run: | 30 | cmake ..\Superbuild -DCMAKE_BUILD_TYPE=Release -G"Visual Studio 15 2017" -Ax64 -DQt5_PATH:PATH="$env:Qt5_Dir" -DBUILD_WITH_PYTHON:BOOL=OFF 31 | 32 | - name: Compile 33 | working-directory: bin 34 | shell: cmd 35 | run: cmake --build . --config Release -j 3 36 | 37 | - name: Package 38 | working-directory: bin/Seg3D 39 | shell: cmd 40 | run: cmake --build . --config Release --target package 41 | 42 | - name: Upload installer 43 | uses: actions/upload-artifact@v2 44 | with: 45 | name: Seg3DWindowsInstaller_${{ matrix.qtversion }} 46 | path: bin/Seg3D/Seg3D2-2.*-win64.exe 47 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/Seg3DWindows/ControllerWindow/ActionsTab.md: -------------------------------------------------------------------------------- 1 | # Actions Tab 2 | 3 | The Actions tab displays all of the actions that have been taken during the Seg3D session. Console entries can also be made with this feature. 4 | 5 | :::{figure-md} fig-on-startup 6 | 7 | ![OnStartup](../../../Seg3DBasicFunctionality_figures/Controller_OnStartup.png) 8 | 9 | Controller Window on initial open. 10 | ::: 11 | 12 | A series of actions area provided in a drop-down menu at the bottom of the window ({numref}`fig-controller-action-list`). Once selected, the action will be placed into a command line to the right of the drop-down menu. 13 | 14 | :::{figure-md} fig-controller-action-list 15 | 16 | ![ControllerActionList](../../../Seg3DBasicFunctionality_figures/Controller_ActionList.png) 17 | 18 | Controller Window action list. 19 | ::: 20 | 21 | The user can then define the parameters for the action, or simply press enter to see what parameters are required to make the action valid. If additional parameters are needed to run the action, they will be displayed in a message in the box below the command line ({numref}`fig-usability-msg`). 22 | 23 | :::{figure-md} fig-usability-msg 24 | 25 | ![UsabilityMsg](../../../Seg3DBasicFunctionality_figures/Controller_UsabilityMsg.png) 26 | 27 | Action usability message. 28 | ::: 29 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/Tools/CropTool.md: -------------------------------------------------------------------------------- 1 | # Crop 2 | 3 | The Crop tool will crop one or more layers to a specified size. This tool will clip multiple layers from the same group to the same size by choosing them in the list of layers near the top of the window. The Crop tool also works on the new Seg3D large volume data layer format. 4 | 5 | ## Detailed Description 6 | 7 | The size of the new volume can be specified using the sliders in the tool window, or by adjusting the widget in the 2D viewing windows. The sliders in the tools window will specify the origin and the size of the cropping region. The buttons over the slider specify which parameter is displayed. It should be noted that you can display the indexed or geometric coordinates by checking/unchecking the *crop in indexed space* option near the bottom of the window. 8 | 9 | The Crop widget is shown as a red box in the 2D viewers. This can be adjusted in any plane by clicking and dragging on the edge to change the size, or in the middle to change the origin. The mouse pointer will change to indicate which function will be affected. Press *Crop* to finish cropping the volumes. 10 | 11 | Currently, data layers should not have more than 4096 pixels in a single dimension, as data layers are not rendered as bricks but as a single texture. 12 | 13 | ![alt text](../images/CropGUI.png) 14 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/DataFilters/ArithmeticFilter.md: -------------------------------------------------------------------------------- 1 | # Arithmetic 2 | 3 | This filter runs basic boolean operations on a pixel by pixel basis. 4 | 5 | ## Detailed Description 6 | 7 | The Arithmetic filter allows the user to run basic arithmetic and boolean operations on both image and mask data on a pixel by pixel basis. This filter can handle up to four inputs and can be used to perform calculate any expression provided by the user (correct syntax is `RESULT = \;`). There are also many saved expressions that exists as separate filters or tools, the main difference is the functionality to handle more than two inputs. 8 | 9 | Any operation can be performed on either type of data, but it should be noted that if a boolean operator is performed it uses zero and non-zero values as the only two possible cases. This applies to using data layers and also values that may be the summation of mask layers. 10 | 11 | This filter also enables outputs of both data and mask layers. The filter will switch the output the match the input if the input is changed, but it can be changed afterward. If there are multiple values in the mathematical result, but mask layer output is chosen, the filter will perform a threshold to try and capture the relevant data in a mask, usually capturing values over zero in the data. 12 | 13 | ![alt text](../images/ArithmeticGUI.png) 14 | -------------------------------------------------------------------------------- /docs/references.bib: -------------------------------------------------------------------------------- 1 | @article{Can1986, 2 | author={Canny, John}, 3 | journal={IEEE Transactions on Pattern Analysis and Machine Intelligence}, 4 | title={A Computational Approach to Edge Detection}, 5 | year={1986}, 6 | volume={PAMI-8}, 7 | number={6}, 8 | pages={679-698}, 9 | doi={10.1109/TPAMI.1986.4767851} 10 | } 11 | 12 | 13 | @article{PM1990, 14 | author={Pietro Perona and Jalhandra Malik}, 15 | journal={IEEE Transactions on Pattern Analysis and Machine Intelligence}, 16 | title={Scale-space and edge detection using anisotropic diffusion}, 17 | year={1990}, 18 | volume={12}, 19 | number={7}, 20 | pages={629-639}, 21 | doi={10.1109/34.56205} 22 | } 23 | 24 | @article{TO2002, 25 | author={Greg Turk and James F. O'Brien}, 26 | title={Modelling with Implicit Surfaces That Interpolate}, 27 | year={2002}, 28 | issue_date={October 2002}, 29 | publisher={Association for Computing Machinery}, 30 | address={New York, NY, USA}, 31 | volume={21}, 32 | number={4}, 33 | issn={0730-0301}, 34 | doi={10.1145/571647.571650}, 35 | journal={ACM Trans. Graph.}, 36 | month=oct, 37 | pages={855–873}, 38 | keywords={modeling, function interpolation, thin-plate techniques, Implicit surfaces} 39 | } 40 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/AdvancedFilters/IntensityCorrection.md: -------------------------------------------------------------------------------- 1 | # Intensity Correction 2 | 3 | This filter attempts to make a homogeneous intensity over the data layer. 4 | 5 | ## Detailed Description 6 | 7 | The Intensity Correction filter attempts to make the intensity over the data layer homogenous. This is very useful when dealing with MR images, as the intensity values and contrast can vary over space due to magnetic field variations. This filter will attempt to fit a spline to average intensity of the image, then to use that spline to equalize the intensity values over the space. 8 | 9 | There are two parameters in this filter, *polynomial order* and *edge sensitivity.* 10 | 11 | The *polynomial order* parameter controls the kind of line used to correct the image. A *polynomial order* of 1 assumes that any changes in intensity is linear through the image. A higher *polynomial order* may be needed if there are more complex patterns of intensity variation, such as seemingly isolated regions of high or low intensities. 12 | 13 | The *edge sensitivity* parameter controls the correction algorithm that prevents artifacts do to edges in the image. The higher the sensitivity, the less the algorithm will correct for edge artifacts. As *edge sensitivity* approaches 0, the algorithm attempts to leave edges unchanged and may suppress the Intensity Correction altogether. 14 | 15 | ![alt text](../images/IntensityCorrectionGUI.png) 16 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/Tools/TransformTool.md: -------------------------------------------------------------------------------- 1 | # Transform 2 | 3 | This tool can be used to translate and scale one or more layers. 4 | 5 | ## Detailed Description 6 | 7 | The Transform tool can be used to translate and scale one or more layers. This tool can be used on both mask layers and image data layers. This tool allows the user to change the origin (translate) and the spacing (scale) of multiple layers in a group. A key use of this tool is to manually transform one layer to match the origin and spacing of a different group, thus including the layer in that group. 8 | 9 | The origin and spacing can be changed in the fields provided, or editing the box widget in the 2D viewer. To change the box widget, **left mouse** click and drag in the middle to move the origin, **left mouse** click and drag on the edge to change the spacing. The aspect ration of the spacing can be fixed (*Keep Aspect Ratio* option) or the spacing dimension can change independently. The Transform parameters can also be reset so that the original origin and spacing are displayed. 10 | 11 | A preview of one of the checked layers from the list will be shown in the 2D viewer, as well as the box widget. Both these can be hidden by unchecking the *show preview* and *show border* options, respectively. If more than one layer is checked, you may choose which layer to preview with the drop down menu provided. 12 | 13 | ![alt text](../images/TransformGUI.png) 14 | -------------------------------------------------------------------------------- /src/Core/VolumeRenderer/VolumeShaderSimple.vert: -------------------------------------------------------------------------------- 1 | // GLSL vertex shader for slice based volume rendering 2 | 3 | uniform bool enable_lighting; 4 | uniform bool enable_fog; 5 | uniform vec3 tex_bbox_min; // Minimum values of texture position in world space 6 | uniform vec3 tex_bbox_size; // Size of texture in world space 7 | 8 | varying vec3 light_dir; // Light direction 9 | varying vec3 half_vector; // Half vector between eye and light source. 10 | // In the case of head light, it's the same as eye vector. 11 | 12 | uniform vec2 fog_range; 13 | varying float fog_depth; 14 | 15 | // Vertex position in world coordinates 16 | varying vec4 world_coord_pos; 17 | 18 | void main() 19 | { 20 | // The position of the vertex in eye space 21 | vec4 eye_coord_pos = gl_ModelViewMatrix * gl_Vertex; 22 | 23 | if ( enable_lighting ) 24 | { 25 | // With headlight, light position is always at the origin in eye space 26 | vec3 aux = vec3( -eye_coord_pos ); 27 | light_dir = normalize( aux ); 28 | half_vector = light_dir; 29 | } 30 | 31 | if ( enable_fog ) 32 | { 33 | fog_depth = ( -eye_coord_pos.z - fog_range[ 0 ] ) / ( fog_range[ 1 ] - fog_range[ 0 ] ); 34 | } 35 | 36 | world_coord_pos = gl_Vertex; 37 | gl_TexCoord[0].stp = (gl_Vertex.xyz - tex_bbox_min)/tex_bbox_size; 38 | gl_ClipVertex = gl_ModelViewMatrix * gl_Vertex; 39 | gl_Position = ftransform(); 40 | } 41 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/Tools/ResampleTool.md: -------------------------------------------------------------------------------- 1 | # Resample 2 | 3 | This tool allows the user to resample one or more volumes to change the resolution. 4 | 5 | ## Detailed Description 6 | 7 | This tool can be used on both mask and data layers. 8 | 9 | The resampling can be set manually using the sliders, or by trying to match the element number of another layer group. To manually choose the resampling, there are options to resample with the same ratio in every direction (check *Constrain Aspect* option) or to resample each direction independently (must uncheck *Constrain Aspect* option to enable). To resample to match another group, you must have another layer group loaded. You may choose the desired group from the drop down menu and the padding value. 10 | 11 | Interpolation of the data is often needed when resampling, especially with image data. There are several options for interpolation in the Resample tool: Box, Tent, Cubic (Catmull-Rom and B-spline), Quartic, and Gaussian which are provided by the Teem library, and Linear, B-spline and Nearest Neighbor from the ITK library. You may choose the interpolation method in the drop down menu near the bottom of the tool window. 12 | 13 | Resampling a layer to match the geometry of another group can also be done by clicking (left mouse button) on a layer while holding down the Shift key, and dragging the layer to the destination group. 14 | 15 | ![alt text](../images/ResampleGUI.png) 16 | -------------------------------------------------------------------------------- /src/Bootstrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # 2 | # For more information, please see: http://software.sci.utah.edu 3 | # 4 | # The MIT License 5 | # 6 | # Copyright (c) 2016 Scientific Computing and Imaging Institute, 7 | # University of Utah. 8 | # 9 | # 10 | # Permission is hereby granted, free of charge, to any person obtaining a 11 | # copy of this software and associated documentation files (the "Software"), 12 | # to deal in the Software without restriction, including without limitation 13 | # the rights to use, copy, modify, merge, publish, distribute, sublicense, 14 | # and/or sell copies of the Software, and to permit persons to whom the 15 | # Software is furnished to do so, subject to the following conditions: 16 | # 17 | # The above copyright notice and this permission notice shall be included 18 | # in all copies or substantial portions of the Software. 19 | # 20 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 21 | # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 22 | # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 23 | # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 24 | # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 25 | # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 26 | # DEALINGS IN THE SOFTWARE. 27 | # 28 | 29 | add_subdirectory(ShaderImporter) 30 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/Seg3DViewer/ControllingWindows.md: -------------------------------------------------------------------------------- 1 | --- 2 | substitutions: 3 | CloseWindow: | 4 | ```{image} ../../Seg3DBasicFunctionality_figures/close_window.png 5 | :class: inline 6 | ``` 7 | 8 | Dock: | 9 | ```{image} ../../Seg3DBasicFunctionality_figures/dock.png 10 | :class: inline 11 | ``` 12 | --- 13 | 14 | # Controlling Windows 15 | 16 | The windows on docked the side of the screen can be any of these five windows: [Project](../Seg3DWindows/ProjectWindow), [Tools](../Seg3DWindows/ToolsWindow), [Layer Manager](../Seg3DWindows/LayerManagerWindow), [Volume Viewer](../Seg3DWindows/VolumeViewWindow/index), and [Provenance](../Seg3DWindows/ProvenanceWindow) windows. Each of these widows can be closed by pressing on the close button {{ CloseWindow }} and opened by choosing the window from the **Window** menu or using hot key. When opened, the window will appear in the last location used, or the default if never opened. The windows can also be detached from the side (by pressing the detach button {{ Dock }} and reattached to the side by moving the window close to the side of the Seg3D window, or by double clicking on the window header. Any detached window can be moved by clicking and dragging on the window header and resized by clicking and dragging on the corner of the window. Attached windows can also be resized by clicking and dragging on border between it and the viewing panels, but are more limited in the changes allowed. 17 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/Tools/PointSetRegistrationTool.md: -------------------------------------------------------------------------------- 1 | # Point Set Register 2 | 3 | This tool will register one mask layer to another. 4 | 5 | ## Detailed Description 6 | 7 | The Point Set Registration tool will register one mask layer to another mask layer. This is currently the only tool or filter that will take inputs from two different layer groups as the main purpose of this tool is to allow the user to map a segmentation from one grid to another with a similar mask layer. The tool attempts to register the entire mask data to another mask data using the iterative closest points method(rigid registration) and will save and display the transform generated for use on the other layers in the registered layer's group. Since this is an iterative method, the user can set the number of iterations. 8 | 9 | To run this registration, choose for the first input the mask layer in the destination frame (to register to) and the mask to change (register) as the second input. The ideas is that these would be in separate layer groups. Clicking the register button will create a new layer in the group of the first input and the transformation will be saved and displayer (translation and rotation). There will be a list of other mask layers from the second input's group with which the user can select the layer on which to perform the saved transform. Upon pressing transform, more layers will be generated in the group of the first input layer. 10 | 11 | ![alt text](../images/PointSetRegisterGUI.png) 12 | -------------------------------------------------------------------------------- /src/QtUtils/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # 2 | # For more information, please see: http://software.sci.utah.edu 3 | # 4 | # The MIT License 5 | # 6 | # Copyright (c) 2016 Scientific Computing and Imaging Institute, 7 | # University of Utah. 8 | # 9 | # 10 | # Permission is hereby granted, free of charge, to any person obtaining a 11 | # copy of this software and associated documentation files (the "Software"), 12 | # to deal in the Software without restriction, including without limitation 13 | # the rights to use, copy, modify, merge, publish, distribute, sublicense, 14 | # and/or sell copies of the Software, and to permit persons to whom the 15 | # Software is furnished to do so, subject to the following conditions: 16 | # 17 | # The above copyright notice and this permission notice shall be included 18 | # in all copies or substantial portions of the Software. 19 | # 20 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 21 | # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 22 | # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 23 | # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 24 | # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 25 | # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 26 | # DEALINGS IN THE SOFTWARE. 27 | # 28 | 29 | 30 | add_subdirectory(Utils) 31 | add_subdirectory(Widgets) 32 | add_subdirectory(Bridge) 33 | -------------------------------------------------------------------------------- /src/Resources/info.plist: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | CFBundleLocalizations 6 | 7 | en 8 | 9 | CFBundleAllowMixedLocalizations 10 | 11 | CFBundleDevelopmentRegion 12 | en_US 13 | CFBundleExecutable 14 | Seg3D2 15 | CFBundleIconFile 16 | Seg3D.icns 17 | CFBundleGetInfoString 18 | Seg3D 2.0.0 - MIT License 19 | CFBundleDocumentTypes 20 | 21 | 22 | NSDocumentClass 23 | Seg3DDataFile 24 | CFBundleTypeRole 25 | Viewer 26 | CFBundleTypeOSTypes 27 | 28 | NRRD 29 | NRD 30 | 31 | CFBundleTypeIconFile 32 | Seg3D.icns 33 | CFBundleTypeName 34 | Nearly Raw Raster Data 35 | CFBundleTypeExtensions 36 | 37 | nrrd 38 | nrd 39 | NRRD 40 | NRD 41 | 42 | LSHandlerRank 43 | Default 44 | 45 | 46 | CFBundleName 47 | Seg3D2 48 | 49 | 50 | -------------------------------------------------------------------------------- /src/CMake/GetGitRevisionDescription.cmake.in: -------------------------------------------------------------------------------- 1 | # 2 | # Internal file for GetGitRevisionDescription.cmake 3 | # 4 | # Requires CMake 2.6 or newer (uses the 'function' command) 5 | # 6 | # Original Author: 7 | # 2009-2010 Ryan Pavlik 8 | # http://academic.cleardefinition.com 9 | # Iowa State University HCI Graduate Program/VRAC 10 | # 11 | # Copyright Iowa State University 2009-2010. 12 | # Distributed under the Boost Software License, Version 1.0. 13 | # (See accompanying file LICENSE_1_0.txt or copy at 14 | # http://www.boost.org/LICENSE_1_0.txt) 15 | 16 | set(HEAD_HASH) 17 | 18 | file(READ "@HEAD_FILE@" HEAD_CONTENTS LIMIT 1024) 19 | 20 | string(STRIP "${HEAD_CONTENTS}" HEAD_CONTENTS) 21 | if(HEAD_CONTENTS MATCHES "ref") 22 | # named branch 23 | string(REPLACE "ref: " "" HEAD_REF "${HEAD_CONTENTS}") 24 | if(EXISTS "@GIT_DIR@/${HEAD_REF}") 25 | configure_file("@GIT_DIR@/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY) 26 | else() 27 | configure_file("@GIT_DIR@/packed-refs" "@GIT_DATA@/packed-refs" COPYONLY) 28 | file(READ "@GIT_DATA@/packed-refs" PACKED_REFS) 29 | if(${PACKED_REFS} MATCHES "([0-9a-z]*) ${HEAD_REF}") 30 | set(HEAD_HASH "${CMAKE_MATCH_1}") 31 | endif() 32 | endif() 33 | else() 34 | # detached HEAD 35 | configure_file("@GIT_DIR@/HEAD" "@GIT_DATA@/head-ref" COPYONLY) 36 | endif() 37 | 38 | if(NOT HEAD_HASH) 39 | file(READ "@GIT_DATA@/head-ref" HEAD_HASH LIMIT 1024) 40 | string(STRIP "${HEAD_HASH}" HEAD_HASH) 41 | endif() 42 | -------------------------------------------------------------------------------- /src/Interface/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # 2 | # For more information, please see: http://software.sci.utah.edu 3 | # 4 | # The MIT License 5 | # 6 | # Copyright (c) 2016 Scientific Computing and Imaging Institute, 7 | # University of Utah. 8 | # 9 | # 10 | # Permission is hereby granted, free of charge, to any person obtaining a 11 | # copy of this software and associated documentation files (the "Software"), 12 | # to deal in the Software without restriction, including without limitation 13 | # the rights to use, copy, modify, merge, publish, distribute, sublicense, 14 | # and/or sell copies of the Software, and to permit persons to whom the 15 | # Software is furnished to do so, subject to the following conditions: 16 | # 17 | # The above copyright notice and this permission notice shall be included 18 | # in all copies or substantial portions of the Software. 19 | # 20 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 21 | # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 22 | # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 23 | # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 24 | # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 25 | # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 26 | # DEALINGS IN THE SOFTWARE. 27 | # 28 | 29 | add_subdirectory(Application) 30 | add_subdirectory(ToolInterface) 31 | #add_subdirectory(ImageRegistrationInterface) 32 | -------------------------------------------------------------------------------- /src/Bootstrap/ShaderImporter/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # 2 | # For more information, please see: http://software.sci.utah.edu 3 | # 4 | # The MIT License 5 | # 6 | # Copyright (c) 2016 Scientific Computing and Imaging Institute, 7 | # University of Utah. 8 | # 9 | # 10 | # Permission is hereby granted, free of charge, to any person obtaining a 11 | # copy of this software and associated documentation files (the "Software"), 12 | # to deal in the Software without restriction, including without limitation 13 | # the rights to use, copy, modify, merge, publish, distribute, sublicense, 14 | # and/or sell copies of the Software, and to permit persons to whom the 15 | # Software is furnished to do so, subject to the following conditions: 16 | # 17 | # The above copyright notice and this permission notice shall be included 18 | # in all copies or substantial portions of the Software. 19 | # 20 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 21 | # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 22 | # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 23 | # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 24 | # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 25 | # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 26 | # DEALINGS IN THE SOFTWARE. 27 | # 28 | 29 | set(SHADER_IMPORTER_SRCS 30 | main.cc 31 | ) 32 | 33 | add_executable(ShaderImporter ${SHADER_IMPORTER_SRCS}) 34 | -------------------------------------------------------------------------------- /src/Core/Renderer/Limits.h: -------------------------------------------------------------------------------- 1 | /* 2 | For more information, please see: http://software.sci.utah.edu 3 | 4 | The MIT License 5 | 6 | Copyright (c) 2016 Scientific Computing and Imaging Institute, 7 | University of Utah. 8 | 9 | 10 | Permission is hereby granted, free of charge, to any person obtaining a 11 | copy of this software and associated documentation files (the "Software"), 12 | to deal in the Software without restriction, including without limitation 13 | the rights to use, copy, modify, merge, publish, distribute, sublicense, 14 | and/or sell copies of the Software, and to permit persons to whom the 15 | Software is furnished to do so, subject to the following conditions: 16 | 17 | The above copyright notice and this permission notice shall be included 18 | in all copies or substantial portions of the Software. 19 | 20 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 21 | OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 22 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 23 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 24 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 25 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 26 | DEALINGS IN THE SOFTWARE. 27 | */ 28 | 29 | #ifndef CORE_RENDERER_LIMITS_H 30 | #define CORE_RENDERER_LIMITS_H 31 | 32 | 33 | namespace RendererLimits 34 | { 35 | const int TextureDim = 4096; 36 | } 37 | 38 | #endif 39 | -------------------------------------------------------------------------------- /src/Core/Utils/Notifier.cc: -------------------------------------------------------------------------------- 1 | /* 2 | For more information, please see: http://software.sci.utah.edu 3 | 4 | The MIT License 5 | 6 | Copyright (c) 2016 Scientific Computing and Imaging Institute, 7 | University of Utah. 8 | 9 | 10 | Permission is hereby granted, free of charge, to any person obtaining a 11 | copy of this software and associated documentation files (the "Software"), 12 | to deal in the Software without restriction, including without limitation 13 | the rights to use, copy, modify, merge, publish, distribute, sublicense, 14 | and/or sell copies of the Software, and to permit persons to whom the 15 | Software is furnished to do so, subject to the following conditions: 16 | 17 | The above copyright notice and this permission notice shall be included 18 | in all copies or substantial portions of the Software. 19 | 20 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 21 | OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 22 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 23 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 24 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 25 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 26 | DEALINGS IN THE SOFTWARE. 27 | */ 28 | 29 | #include 30 | 31 | namespace Core 32 | { 33 | 34 | Notifier::Notifier() 35 | { 36 | } 37 | 38 | Notifier::~Notifier() 39 | { 40 | } 41 | 42 | } // end namespace Core 43 | -------------------------------------------------------------------------------- /src/Core/Python/ToPythonConverters.h: -------------------------------------------------------------------------------- 1 | /* 2 | For more information, please see: http://software.sci.utah.edu 3 | 4 | The MIT License 5 | 6 | Copyright (c) 2016 Scientific Computing and Imaging Institute, 7 | University of Utah. 8 | 9 | 10 | Permission is hereby granted, free of charge, to any person obtaining a 11 | copy of this software and associated documentation files (the "Software"), 12 | to deal in the Software without restriction, including without limitation 13 | the rights to use, copy, modify, merge, publish, distribute, sublicense, 14 | and/or sell copies of the Software, and to permit persons to whom the 15 | Software is furnished to do so, subject to the following conditions: 16 | 17 | The above copyright notice and this permission notice shall be included 18 | in all copies or substantial portions of the Software. 19 | 20 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 21 | OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 22 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 23 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 24 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 25 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 26 | DEALINGS IN THE SOFTWARE. 27 | */ 28 | 29 | #ifndef CORE_PYTHON_TOPYTHONCONVERTERS_H 30 | #define CORE_PYTHON_TOPYTHONCONVERTERS_H 31 | 32 | namespace Core 33 | { 34 | void RegisterToPythonConverters(); 35 | } 36 | 37 | #endif 38 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/AdvancedFilters/CannyEdge.md: -------------------------------------------------------------------------------- 1 | # Canny Edge 2 | 3 | This filter will output the pixels that are edges in a mask layer. 4 | 5 | ## Detailed Description 6 | 7 | The Canny Edge filter computes the edges in a data layer using a Canny Edge Detection Filter {cite:p}`Can1986`. This filter will output the pixels that are edges in a mask layer. 8 | 9 | This filter is composed of four steps: 10 | 11 | 1. Smooth the input image with Gaussian filter. 12 | 2. calculate the second directional derivatives of the smoothed image. 13 | 3. Non-Maximum Suppression: the zero-crossings of the 2nd derivative are found, and the sign of the third derivative is used to find the correct extrema. 14 | 4. The hysteresis thresholding is applied to the Gradient Magnitude (multiplied with zero-crossings) of the smoothed image to find the link edges. 15 | 16 | There are two parameters for this filter, *distance* and *minimum threshold*. The *distance* parameter is the controls the Gaussian blurring in the first step and is the same as in the Gaussian blur filter. Higher distance will result in fewer edges detected and the edges that are detected will likely be thicker. This is because these edges are being blurred out. The *minimum threshold* parameter controls the hysteresis thresholding in the fourth step. This parameter will set the level of that will count as an edge or not. This means that a higher minimum threshold will have fewer edges in the result and the remaining edges while more likely be true edges. 17 | 18 | ![alt text](../images/CannyEdgeGUI.png) 19 | -------------------------------------------------------------------------------- /src/Core/DataBlock/ITKImageData.cc: -------------------------------------------------------------------------------- 1 | /* 2 | For more information, please see: http://software.sci.utah.edu 3 | 4 | The MIT License 5 | 6 | Copyright (c) 2016 Scientific Computing and Imaging Institute, 7 | University of Utah. 8 | 9 | 10 | Permission is hereby granted, free of charge, to any person obtaining a 11 | copy of this software and associated documentation files (the "Software"), 12 | to deal in the Software without restriction, including without limitation 13 | the rights to use, copy, modify, merge, publish, distribute, sublicense, 14 | and/or sell copies of the Software, and to permit persons to whom the 15 | Software is furnished to do so, subject to the following conditions: 16 | 17 | The above copyright notice and this permission notice shall be included 18 | in all copies or substantial portions of the Software. 19 | 20 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 21 | OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 22 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 23 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 24 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 25 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 26 | DEALINGS IN THE SOFTWARE. 27 | */ 28 | 29 | // Core includes 30 | #include 31 | 32 | namespace Core 33 | { 34 | 35 | ITKImageData::ITKImageData() 36 | { 37 | } 38 | 39 | ITKImageData::~ITKImageData() 40 | { 41 | } 42 | 43 | } // end namespace Core 44 | -------------------------------------------------------------------------------- /src/Core/RenderResources/RenderContext.cc: -------------------------------------------------------------------------------- 1 | /* 2 | For more information, please see: http://software.sci.utah.edu 3 | 4 | The MIT License 5 | 6 | Copyright (c) 2016 Scientific Computing and Imaging Institute, 7 | University of Utah. 8 | 9 | 10 | Permission is hereby granted, free of charge, to any person obtaining a 11 | copy of this software and associated documentation files (the "Software"), 12 | to deal in the Software without restriction, including without limitation 13 | the rights to use, copy, modify, merge, publish, distribute, sublicense, 14 | and/or sell copies of the Software, and to permit persons to whom the 15 | Software is furnished to do so, subject to the following conditions: 16 | 17 | The above copyright notice and this permission notice shall be included 18 | in all copies or substantial portions of the Software. 19 | 20 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 21 | OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 22 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 23 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 24 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 25 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 26 | DEALINGS IN THE SOFTWARE. 27 | */ 28 | 29 | #include 30 | 31 | namespace Core 32 | { 33 | 34 | RenderContext::RenderContext() 35 | { 36 | } 37 | 38 | RenderContext::~RenderContext() 39 | { 40 | } 41 | 42 | } // end namespace Core 43 | 44 | -------------------------------------------------------------------------------- /src/Core/DataBlock/ITKImage2DData.cc: -------------------------------------------------------------------------------- 1 | /* 2 | For more information, please see: http://software.sci.utah.edu 3 | 4 | The MIT License 5 | 6 | Copyright (c) 2016 Scientific Computing and Imaging Institute, 7 | University of Utah. 8 | 9 | 10 | Permission is hereby granted, free of charge, to any person obtaining a 11 | copy of this software and associated documentation files (the "Software"), 12 | to deal in the Software without restriction, including without limitation 13 | the rights to use, copy, modify, merge, publish, distribute, sublicense, 14 | and/or sell copies of the Software, and to permit persons to whom the 15 | Software is furnished to do so, subject to the following conditions: 16 | 17 | The above copyright notice and this permission notice shall be included 18 | in all copies or substantial portions of the Software. 19 | 20 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 21 | OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 22 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 23 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 24 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 25 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 26 | DEALINGS IN THE SOFTWARE. 27 | */ 28 | 29 | // Core includes 30 | #include 31 | 32 | namespace Core 33 | { 34 | 35 | ITKImage2DData::ITKImage2DData() 36 | { 37 | } 38 | 39 | ITKImage2DData::~ITKImage2DData() 40 | { 41 | } 42 | 43 | } // end namespace Core 44 | -------------------------------------------------------------------------------- /src/Application/Filters/Utils/PadValues.cc: -------------------------------------------------------------------------------- 1 | /* 2 | For more information, please see: http://software.sci.utah.edu 3 | 4 | The MIT License 5 | 6 | Copyright (c) 2016 Scientific Computing and Imaging Institute, 7 | University of Utah. 8 | 9 | 10 | Permission is hereby granted, free of charge, to any person obtaining a 11 | copy of this software and associated documentation files (the "Software"), 12 | to deal in the Software without restriction, including without limitation 13 | the rights to use, copy, modify, merge, publish, distribute, sublicense, 14 | and/or sell copies of the Software, and to permit persons to whom the 15 | Software is furnished to do so, subject to the following conditions: 16 | 17 | The above copyright notice and this permission notice shall be included 18 | in all copies or substantial portions of the Software. 19 | 20 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 21 | OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 22 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 23 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 24 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 25 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 26 | DEALINGS IN THE SOFTWARE. 27 | */ 28 | 29 | #include 30 | 31 | namespace Filter { 32 | 33 | const std::string PadValues::ZERO_C( "0" ); 34 | const std::string PadValues::MIN_C( "min" ); 35 | const std::string PadValues::MAX_C( "max" ); 36 | 37 | } 38 | -------------------------------------------------------------------------------- /docs/user_docs/Manuals/Functions/Seg3DWindows/VolumeViewWindow/TransferFunction.md: -------------------------------------------------------------------------------- 1 | # Transfer Function 2 | 3 | Within the transfer function pane, a histogram exists that defines the volumetric image. The transfer function can be displayed on a Linear or Logarithmic scale. In the transfer function window, the user can choose to add or delete a feature. A feature can be dragged into positions defining regions of the histogram that the user wants to render. The default Feature is a line. By clicking and dragging the line, the feature can be moved. By clicking a point on the line, the individual point can be moved. Additional points can be added to a feature by clicking anywhere in the histogram panel that is not already defined by a line, that is, in the gray or black regions. 4 | 5 | Each of the features observed can also be enabled/disabled and viewed as solid or graded. The solid feature (as addressed above) allows the feature to be represented as a graded slice or as a solid one. Solid slices simply apply the same color saturation to each section of the volume slice. De-selecting the solid option applies a gradient to the slices, with the outer edge being the brightest color. 6 | 7 | Each point and feature can be repositioned, reshaped, and recolored in order to distinguish between defined regions. To change the color of a feature, select the desired feature and adjust the slider regions below the histogram in the Red/Green/Blue features. Colors can be used to easily distinguish different features in the volume. Additionally, each features Ambient and Specular lighting can be adjusted as well as volume shininess is adjustable 8 | -------------------------------------------------------------------------------- /src/Core/Action/ActionParameter.cc: -------------------------------------------------------------------------------- 1 | /* 2 | For more information, please see: http://software.sci.utah.edu 3 | 4 | The MIT License 5 | 6 | Copyright (c) 2016 Scientific Computing and Imaging Institute, 7 | University of Utah. 8 | 9 | 10 | Permission is hereby granted, free of charge, to any person obtaining a 11 | copy of this software and associated documentation files (the "Software"), 12 | to deal in the Software without restriction, including without limitation 13 | the rights to use, copy, modify, merge, publish, distribute, sublicense, 14 | and/or sell copies of the Software, and to permit persons to whom the 15 | Software is furnished to do so, subject to the following conditions: 16 | 17 | The above copyright notice and this permission notice shall be included 18 | in all copies or substantial portions of the Software. 19 | 20 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 21 | OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 22 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 23 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 24 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 25 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 26 | DEALINGS IN THE SOFTWARE. 27 | */ 28 | 29 | #include 30 | 31 | namespace Core 32 | { 33 | 34 | ActionParameterBase::ActionParameterBase() : 35 | persistent_( true ) 36 | { 37 | } 38 | 39 | ActionParameterBase::~ActionParameterBase() 40 | { 41 | } 42 | 43 | } // namespace Core 44 | -------------------------------------------------------------------------------- /src/Core/State/StateViewBase.cc: -------------------------------------------------------------------------------- 1 | /* 2 | For more information, please see: http://software.sci.utah.edu 3 | 4 | The MIT License 5 | 6 | Copyright (c) 2016 Scientific Computing and Imaging Institute, 7 | University of Utah. 8 | 9 | 10 | Permission is hereby granted, free of charge, to any person obtaining a 11 | copy of this software and associated documentation files (the "Software"), 12 | to deal in the Software without restriction, including without limitation 13 | the rights to use, copy, modify, merge, publish, distribute, sublicense, 14 | and/or sell copies of the Software, and to permit persons to whom the 15 | Software is furnished to do so, subject to the following conditions: 16 | 17 | The above copyright notice and this permission notice shall be included 18 | in all copies or substantial portions of the Software. 19 | 20 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 21 | OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 22 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 23 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 24 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 25 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 26 | DEALINGS IN THE SOFTWARE. 27 | */ 28 | 29 | #include 30 | 31 | namespace Core 32 | { 33 | 34 | StateViewBase::StateViewBase( const std::string& stateid ) : 35 | StateBase( stateid ) 36 | { 37 | } 38 | 39 | StateViewBase::~StateViewBase() 40 | { 41 | } 42 | 43 | } // end namespace Core 44 | 45 | -------------------------------------------------------------------------------- /docs/user_docs/Tools/Tools/MeasurementTool.md: -------------------------------------------------------------------------------- 1 | # Measure 2 | 3 | The Measure tool will calculate the distance between two points chosen in the viewer windows. The points, line segments, and measurements in the 2D viewers and record the measurements in a table in the tools window. This tool will calculate and retain several different distances allowing the user to copy the measurements to other software (as a text or into a spreadsheet) using the two copy functions in the tool window (*selection* or *all data*). 4 | 5 | ## Detailed Description 6 | 7 | The user can choose which measurements are visible, change the color, name, and add comments of each of the measurements by **double clicking** on the parameter in the table, or by highlighting the measurement in the able and clicking the active measurement tab. A new measurement automatically becomes active. Using this tab, the user can also center all the active viewers (with picking form other planes allowed) on the points that are in the measurement. 8 | 9 | Back in the general tab, the active layer can be deleted and the opacity of the visualizations in the viewers can be adjusted. Both tabs allow switching between pixel (indexed) and actual (geometric) distances. When this is changed in the active measurement tab, it changes all the measurements. 10 | 11 | ```{list-table} Keyboard and Mouse Actions in the for the Measure Tool 12 | :widths: 25 75 13 | :width: 100% 14 | :header-rows: 1 15 | 16 | * - Action 17 | - Function 18 | 19 | * - ctrl/cmd 20 | - snap to axis 21 | 22 | * - middle mouse button 23 | - snap to slice 24 | 25 | ``` 26 | 27 | ![alt text](../images/MeasureGUI.png) 28 | -------------------------------------------------------------------------------- /src/Core/RenderResources/RenderResourcesContext.cc: -------------------------------------------------------------------------------- 1 | /* 2 | For more information, please see: http://software.sci.utah.edu 3 | 4 | The MIT License 5 | 6 | Copyright (c) 2016 Scientific Computing and Imaging Institute, 7 | University of Utah. 8 | 9 | 10 | Permission is hereby granted, free of charge, to any person obtaining a 11 | copy of this software and associated documentation files (the "Software"), 12 | to deal in the Software without restriction, including without limitation 13 | the rights to use, copy, modify, merge, publish, distribute, sublicense, 14 | and/or sell copies of the Software, and to permit persons to whom the 15 | Software is furnished to do so, subject to the following conditions: 16 | 17 | The above copyright notice and this permission notice shall be included 18 | in all copies or substantial portions of the Software. 19 | 20 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 21 | OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 22 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 23 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 24 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 25 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 26 | DEALINGS IN THE SOFTWARE. 27 | */ 28 | 29 | #include 30 | 31 | namespace Core 32 | { 33 | 34 | RenderResourcesContext::RenderResourcesContext() 35 | { 36 | } 37 | 38 | RenderResourcesContext::~RenderResourcesContext() 39 | { 40 | } 41 | 42 | } // end namespace Core 43 | 44 | --------------------------------------------------------------------------------