├── .github ├── build.sh ├── setup.sh └── workflows │ ├── build-main.yml │ └── build-pr.yml ├── .gitignore ├── LICENSE.txt ├── README.md ├── TODO ├── pom.xml └── src └── main ├── java ├── Align_Image.java ├── AmiraMeshReader_.java ├── AmiraMeshWriter_.java ├── AmiraTableWriter_.java ├── Average_Color.java ├── Bilateral_Filter.java ├── Biorad_Reader.java ├── Biorad_Writer.java ├── CollectGarbage_.java ├── Compute_Curvatures.java ├── CropEditor_.java ├── Delaunay_Voronoi.java ├── Despeckle_.java ├── Fill_holes.java ├── FindIt_.java ├── Implicit_Interpolate_Binary.java ├── KD_Cartoon.java ├── MC_Test.java ├── Menu_Font.java ├── Moving_Least_Squares.java ├── Psychomorph_TEM_Reader.java ├── RGB_to_CIELAB.java ├── ROIBrush_.java ├── ROI_3D.java ├── Replace_Value.java ├── Reslice_Z.java ├── Rohlfing_SBA.java ├── Scrollable_StackWindow.java ├── Seam_Remover.java ├── Segmentation_Editor.java ├── ShowAmiraSurface_.java ├── Show_Label_Centers.java ├── Test_Java3D.java ├── Triangle_Algorithm.java ├── Two_Point_Correlation.java ├── VIB_Protocol.java ├── Visual_Grep.java ├── features │ ├── Hessian_CP_Measures.java │ ├── Sigma_Palette.java │ ├── Surfaceness_.java │ ├── TestComputeCurvatures_.java │ └── Tubeness_.java ├── landmarks │ ├── Affine_From_Landmarks.java │ ├── Bookstein_From_Landmarks.java │ ├── Name_Points.java │ └── Rigid_From_Landmarks.java ├── leica │ ├── Leica_SP_Reader.java │ └── Leica_SP_Writer.java ├── marchingcubes │ └── ExportMesh_.java ├── math3d │ └── Transform_IO.java ├── oldsegmenters │ ├── LabelBrush_.java │ ├── LabelInterpolator_.java │ ├── LabelThresholder_.java │ ├── Segmentator_.java │ └── Segmenter_.java ├── process3d │ ├── Convolve_3d.java │ ├── Dilate_.java │ ├── Distance_Transform_3D.java │ ├── Erode_.java │ ├── FFT_.java │ ├── Find_Minima.java │ ├── Flood_Fill.java │ ├── Gradient_.java │ ├── Harris_Corner_Detector.java │ ├── IFT_.java │ ├── Laplace_.java │ ├── Maximum_.java │ ├── Median_.java │ ├── Minimum_.java │ ├── Particle_Analyzer_3D.java │ ├── Plot_Dots.java │ └── Rebin_.java ├── stacks │ ├── ThreePaneContainer_.java │ ├── ThreePanes_.java │ ├── Three_Pane_Crop.java │ └── Unpack_To_PNG.java ├── textureByRef │ ├── Texture_By_Ref.java │ ├── Texture_By_Ref_col.java │ └── Volume_Editor.java ├── util │ ├── Average_Torsten_Results.java │ ├── Count_Labels.java │ ├── Exposure_Blend_Two_Stacks.java │ ├── Find_Connected_Regions.java │ ├── Histogram_2D.java │ ├── Just_Certain_Labels.java │ ├── Mask_Of_Nearby_Points.java │ ├── Meshes_From_Label_File.java │ ├── Overlay_Registered.java │ ├── Quantile_Based_Normalization.java │ └── RGB_to_Luminance.java ├── vib │ ├── AugmentedLandmarkWarp_.java │ ├── AverageBrain_.java │ ├── Average_Images.java │ ├── BatchLog_.java │ ├── Center_Transformation.java │ ├── Deformable_Registration.java │ ├── DiffusionInterpol2_.java │ ├── EdgeDetectors_.java │ ├── EditAmiraParameters_.java │ ├── ElasticTransform_.java │ ├── Extract_Surface.java │ ├── Fit_Sphere.java │ ├── IDT_Interpolate_Binary.java │ ├── LocalRigidRegistration_.java │ ├── Local_Threshold.java │ ├── MaxEntQuantization_.java │ ├── Points_Dialog.java │ ├── Raster_Rigid.java │ ├── Relabel_.java │ ├── Resample_.java │ ├── RigidRegistration_.java │ ├── SegmentationViewer_.java │ ├── Show_centers.java │ ├── TissueStatistics_.java │ ├── edge │ │ └── Dirichlet_Edge.java │ └── oldregistration │ │ └── PCA_Registration.java └── video │ └── Edit_Video.java └── resources ├── ImageJ3DMacro.txt ├── LICENSE.VIB ├── README.VIB └── plugins.config /.github/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fiji/VIB/HEAD/.github/build.sh -------------------------------------------------------------------------------- /.github/setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fiji/VIB/HEAD/.github/setup.sh -------------------------------------------------------------------------------- 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