├── .gitignore ├── .gitlab-ci-ok.yml ├── .gitlab-ci.yml ├── LICENSE ├── META-INF └── MANIFEST.MF ├── README.md ├── pom.xml ├── src ├── .directory └── main │ ├── java │ ├── META-INF │ │ └── MANIFEST.MF │ └── mcib3d │ │ ├── Classification │ │ ├── Attributes.java │ │ ├── Classifier.java │ │ ├── Data.java │ │ └── DataSet.java │ │ ├── Jama │ │ ├── CholeskyDecomposition.java │ │ ├── EigenvalueDecomposition.java │ │ ├── LUDecomposition.java │ │ ├── Matrix.java │ │ ├── QRDecomposition.java │ │ ├── SingularValueDecomposition.java │ │ ├── test │ │ │ └── TestMatrix.java │ │ └── util │ │ │ └── Maths.java │ │ ├── align │ │ ├── Align2D.java │ │ └── Align3D.java │ │ ├── ext │ │ ├── Imod.java │ │ ├── ImodConf.java │ │ ├── Xmipp.java │ │ └── XmippConf.java │ │ ├── geom │ │ ├── ComparatorBorderDistance.java │ │ ├── ComparatorVoxel.java │ │ ├── GeomTransform3D.java │ │ ├── Gradient.java │ │ ├── GradientPoint.java │ │ ├── IntCoord3D.java │ │ ├── MereoAnalysis.java │ │ ├── MereoObject3D.java │ │ ├── MeshEditor.java │ │ ├── Object3D.java │ │ ├── Object3DFactory.java │ │ ├── Object3DFuzzy.java │ │ ├── Object3DLabel.java │ │ ├── Object3DPoint.java │ │ ├── Object3DSurface.java │ │ ├── Object3DVoxels.java │ │ ├── Object3D_IJUtils.java │ │ ├── ObjectCreator3D.java │ │ ├── ObjectDistBB.java │ │ ├── Objects3DPopulation.java │ │ ├── Objects3DPopulationAnalysis.java │ │ ├── Objects3DPopulationColocalisation.java │ │ ├── Objects3DPopulationInteractions.java │ │ ├── ObjectsPopulationDistances.java │ │ ├── PairColocalisation.java │ │ ├── Point3D.java │ │ ├── Point3DInt.java │ │ ├── RDAR.java │ │ ├── Vector3D.java │ │ ├── Viewer3D_Utils.java │ │ ├── Voxel3D.java │ │ ├── Voxel3DComparable.java │ │ ├── deformation3d │ │ │ ├── DeformableMesh.java │ │ │ ├── Deriche.java │ │ │ ├── IO.java │ │ │ ├── Mesh.java │ │ │ ├── Triangle.java │ │ │ └── Vertex.java │ │ └── interactions │ │ │ ├── Interactions.java │ │ │ ├── InteractionsCompute.java │ │ │ ├── InteractionsComputeContours.java │ │ │ ├── InteractionsComputeDamLines.java │ │ │ ├── InteractionsComputeDilate.java │ │ │ ├── InteractionsComputeVoronoi.java │ │ │ └── InteractionsList.java │ │ ├── geom2 │ │ ├── BoundingBox.java │ │ ├── Object3DComputation.java │ │ ├── Object3DInt.java │ │ ├── Object3DPlane.java │ │ ├── Objects3DIntPopulation.java │ │ ├── TestGeom2.java │ │ ├── VoxelInt.java │ │ └── measurements │ │ │ ├── MeasureAbstract.java │ │ │ ├── MeasureCentroid.java │ │ │ ├── MeasureCompactness.java │ │ │ ├── MeasureDistancesCenter.java │ │ │ ├── MeasureEllipsoid.java │ │ │ ├── MeasureFeret.java │ │ │ ├── MeasureIntensity.java │ │ │ ├── MeasureMoments.java │ │ │ ├── MeasureSurface.java │ │ │ └── MeasureVolume.java │ │ ├── image3d │ │ ├── BlankMask.java │ │ ├── Coordinate3D.java │ │ ├── ImageByte.java │ │ ├── ImageFloat.java │ │ ├── ImageHandler.java │ │ ├── ImageInt.java │ │ ├── ImageLabeller.java │ │ ├── ImageLabeller2D.java │ │ ├── ImagePlus_Utils.java │ │ ├── ImageShort.java │ │ ├── ImageStats.java │ │ ├── IterativeThresholding │ │ │ ├── BestCriteriaMax.java │ │ │ ├── BestCriteriaMin.java │ │ │ ├── BestCriteriaStable.java │ │ │ ├── BestCriterion.java │ │ │ ├── ComparatorObjectTrack.java │ │ │ ├── Criterion.java │ │ │ ├── CriterionClassification.java │ │ │ ├── CriterionCompactness.java │ │ │ ├── CriterionEdge.java │ │ │ ├── CriterionElongation.java │ │ │ ├── CriterionVolume.java │ │ │ ├── ObjectTrack.java │ │ │ └── TrackThreshold.java │ │ ├── MaskIterator.java │ │ ├── Segment3DImage.java │ │ ├── Segment3DSpots.java │ │ ├── comparator │ │ │ ├── ComparatorByte.java │ │ │ ├── ComparatorFloat.java │ │ │ ├── ComparatorInvByte.java │ │ │ ├── ComparatorInvFloat.java │ │ │ ├── ComparatorInvShort.java │ │ │ └── ComparatorShort.java │ │ ├── distanceMap3d │ │ │ ├── CleanUpLocalThickness.java │ │ │ ├── DistanceRidge.java │ │ │ ├── EDT.java │ │ │ ├── EDT_1D.java │ │ │ ├── EdtByte.java │ │ │ ├── EdtByteInv.java │ │ │ ├── EdtFloat.java │ │ │ ├── EdtFloatInv.java │ │ │ ├── EdtShort.java │ │ │ ├── EdtShortInv.java │ │ │ ├── EdtShortLabel.java │ │ │ ├── LocalThickness.java │ │ │ └── VoxEVF.java │ │ ├── legacy │ │ │ ├── ColorImage3D.java │ │ │ ├── FHTImage3D.java │ │ │ ├── Image3D.java │ │ │ ├── IntImage3D.java │ │ │ └── RealImage3D.java │ │ ├── processing │ │ │ ├── BinaryMorpho.java │ │ │ ├── CannyDeriche1D.java │ │ │ ├── CannyEdge3D.java │ │ │ ├── Density3D.java │ │ │ ├── FastArithmetic3D.java │ │ │ ├── FastFilters3D.java │ │ │ ├── FastOperation3D.java │ │ │ ├── FillHoles2D.java │ │ │ ├── FillHoles3D.java │ │ │ ├── Flood3D.java │ │ │ ├── ImageColocalizer.java │ │ │ ├── ManualSpot.form │ │ │ ├── ManualSpot.java │ │ │ ├── MaximaFinder.java │ │ │ └── SymmetryFilter.java │ │ └── regionGrowing │ │ │ ├── AllRegionsAssociation.java │ │ │ ├── AssociationRegion.java │ │ │ ├── Cluster.java │ │ │ ├── RegionGrowing.java │ │ │ ├── Watershed3D.java │ │ │ ├── Watershed3DVoronoi.java │ │ │ └── Watershed3D_old.java │ │ ├── spatial │ │ ├── analysis │ │ │ └── SpatialStatistics.java │ │ ├── descriptors │ │ │ ├── F_Function.java │ │ │ ├── G_Border.java │ │ │ ├── G_Function.java │ │ │ ├── H_Border.java │ │ │ ├── H_Function.java │ │ │ ├── K_Function.java │ │ │ └── SpatialDescriptor.java │ │ └── sampler │ │ │ ├── SpatialModel.java │ │ │ ├── SpatialRandom.java │ │ │ ├── SpatialRandomHardCore.java │ │ │ └── SpatialShuffle.java │ │ ├── tracking_dev │ │ ├── Association.java │ │ ├── AssociationCost.java │ │ ├── AssociationPair.java │ │ ├── Association_Track_Plugin.java │ │ ├── CostColoc2.java │ │ ├── CostColocalisation.java │ │ ├── CostPairMitosis.java │ │ ├── CostTouching.java │ │ ├── HungarianAlgorithm.java │ │ ├── Mitosis.java │ │ ├── MitosisDetector.java │ │ └── TrackingAssociation.java │ │ └── utils │ │ ├── AboutMCIB.java │ │ ├── ArrayUtil.java │ │ ├── CDFTools.java │ │ ├── CheckInstall.java │ │ ├── Chrono.java │ │ ├── HistogramUtil.java │ │ ├── KDTreeC.java │ │ ├── Logger │ │ ├── AbstractLog.java │ │ ├── IJLog.java │ │ ├── IJStatus.java │ │ ├── NoLog.java │ │ └── TextLog.java │ │ ├── Message.java │ │ ├── Shell.java │ │ ├── StackFolderOpener.java │ │ ├── ThreadRunner.java │ │ ├── ThreadUtil.java │ │ └── exceptionPrinter.java │ └── resources │ ├── gpl.txt │ └── icons │ ├── SU.png │ └── suite.png └── target └── mcib3d-core-3.96.31.jar /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mcib3d/mcib3d-core/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitlab-ci-ok.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mcib3d/mcib3d-core/HEAD/.gitlab-ci-ok.yml -------------------------------------------------------------------------------- /.gitlab-ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mcib3d/mcib3d-core/HEAD/.gitlab-ci.yml 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