├── .github ├── build.sh ├── setup.sh └── workflows │ ├── build-main.yml │ └── build-pr.yml ├── .gitignore ├── LICENSE.txt ├── README.md ├── pom.xml └── src └── main ├── java ├── fiji │ └── plugin │ │ ├── Apply_External_Transformation.java │ │ ├── Bead_Registration.java │ │ ├── Multi_View_Deconvolution.java │ │ ├── Multi_View_Fusion.java │ │ └── timelapsedisplay │ │ ├── FileOpenMenuEntry.java │ │ ├── GraphFrame.java │ │ ├── MouseListenerTimelapse.java │ │ ├── RegistrationStatistics.java │ │ └── TimeLapseDisplay.java ├── mpicbg │ ├── icp │ │ ├── ICP.java │ │ ├── PointMatchIdentification.java │ │ └── SimplePointMatchIdentification.java │ ├── pointdescriptor │ │ ├── AbstractPointDescriptor.java │ │ ├── LinkedPoint.java │ │ ├── LocalCoordinateSystemPointDescriptor.java │ │ ├── ModelPointDescriptor.java │ │ ├── SimplePointDescriptor.java │ │ ├── exception │ │ │ └── NoSuitablePointsException.java │ │ ├── matcher │ │ │ ├── Matcher.java │ │ │ ├── ModelPriorMatcher.java │ │ │ ├── ModelPriorSubsetMatcher.java │ │ │ ├── Quaternion.java │ │ │ ├── SimpleMatcher.java │ │ │ └── SubsetMatcher.java │ │ ├── model │ │ │ ├── FixedModel.java │ │ │ ├── TranslationInvariantAffineModel3D.java │ │ │ ├── TranslationInvariantFixedModel.java │ │ │ ├── TranslationInvariantModel.java │ │ │ ├── TranslationInvariantRigidModel2D.java │ │ │ ├── TranslationInvariantRigidModel3D.java │ │ │ └── TranslationInvariantSimilarityModel3D.java │ │ ├── similarity │ │ │ ├── LinearDistance.java │ │ │ ├── ManhattanDistance.java │ │ │ ├── SimilarityMeasure.java │ │ │ └── SquareDistance.java │ │ └── test │ │ │ ├── PointNode.java │ │ │ ├── TestPointDescriptor.java │ │ │ └── VirtualPointNode.java │ ├── spim │ │ ├── ClusterReconstruction.java │ │ ├── Reconstruction.java │ │ ├── fusion │ │ │ ├── AverageContent.java │ │ │ ├── AverageContentFactory.java │ │ │ ├── Blending.java │ │ │ ├── BlendingFactory.java │ │ │ ├── BlendingSimple.java │ │ │ ├── BlendingSimpleFactory.java │ │ │ ├── CombinedPixelWeightener.java │ │ │ ├── CombinedPixelWeightenerFactory.java │ │ │ ├── EntropyFast.java │ │ │ ├── EntropyFastFactory.java │ │ │ ├── FusionControl.java │ │ │ ├── GaussContent.java │ │ │ ├── GaussContentFactory.java │ │ │ ├── IsolatedPixelWeightener.java │ │ │ ├── IsolatedPixelWeightenerFactory.java │ │ │ ├── MappingFusionParalell.java │ │ │ ├── MappingFusionParalellMaxWeight.java │ │ │ ├── MappingFusionSequential.java │ │ │ ├── MappingFusionSequentialDifferentOutput.java │ │ │ ├── PreDeconvolutionFusion.java │ │ │ ├── PreDeconvolutionFusionInterface.java │ │ │ ├── PreDeconvolutionFusionSequential.java │ │ │ ├── SPIMImageFusion.java │ │ │ └── entropy │ │ │ │ ├── Entropy.java │ │ │ │ └── EntropyFloatArray3D.java │ │ ├── io │ │ │ ├── ConfigurationParserException.java │ │ │ ├── ConfigurationParserGeneral.java │ │ │ ├── ConfigurationParserObject.java │ │ │ ├── ConfigurationParserSPIM.java │ │ │ ├── IOFunctions.java │ │ │ ├── ImgLibSaver.java │ │ │ ├── ParsePattern.java │ │ │ ├── ProgramConfiguration.java │ │ │ ├── SPIMConfiguration.java │ │ │ ├── TextFileAccess.java │ │ │ └── XMLFunctions.java │ │ ├── mpicbg │ │ │ ├── Java3d.java │ │ │ ├── PointMatchGeneric.java │ │ │ ├── SketchTikZFileObject.java │ │ │ ├── TileConfigurationPhaseCorrelation.java │ │ │ ├── TileConfigurationSPIM.java │ │ │ └── TileSPIM.java │ │ ├── postprocessing │ │ │ ├── deconvolution │ │ │ │ ├── ExtractPSF.java │ │ │ │ ├── LucyRichardsonFFT.java │ │ │ │ └── LucyRichardsonMultiViewDeconvolution.java │ │ │ └── deconvolution2 │ │ │ │ ├── AdjustInput.java │ │ │ │ ├── BayesMVDeconvolution.java │ │ │ │ ├── Block.java │ │ │ │ ├── CUDATools.java │ │ │ │ ├── Deconvolver.java │ │ │ │ ├── LRFFT.java │ │ │ │ ├── LRFFTThreads.java │ │ │ │ └── LRInput.java │ │ ├── preprocessing │ │ │ └── AutomaticAngleSetup.java │ │ ├── registration │ │ │ ├── ViewDataBeads.java │ │ │ ├── ViewStructure.java │ │ │ ├── bead │ │ │ │ ├── Bead.java │ │ │ │ ├── BeadIdentification.java │ │ │ │ ├── BeadRegistration.java │ │ │ │ ├── BeadSegmentation.java │ │ │ │ ├── BeadStructure.java │ │ │ │ ├── SegmentationBenchmark.java │ │ │ │ ├── error │ │ │ │ │ ├── GlobalErrorStatistics.java │ │ │ │ │ ├── GlobalErrorStatisticsImpl.java │ │ │ │ │ ├── ViewErrorPairWise.java │ │ │ │ │ └── ViewErrorStatistics.java │ │ │ │ └── laplace │ │ │ │ │ ├── DoGMaximum.java │ │ │ │ │ ├── LaPlaceFunctions.java │ │ │ │ │ └── RejectStatistics.java │ │ │ ├── detection │ │ │ │ ├── AbstractDetection.java │ │ │ │ ├── Detection.java │ │ │ │ ├── DetectionIdentification.java │ │ │ │ ├── DetectionRegistration.java │ │ │ │ ├── DetectionSegmentation.java │ │ │ │ ├── DetectionStructure.java │ │ │ │ ├── DetectionView.java │ │ │ │ └── descriptor │ │ │ │ │ ├── CoordSystem3d.java │ │ │ │ │ ├── CoordSystemSecure3d.java │ │ │ │ │ ├── CorrespondenceExtraction.java │ │ │ │ │ ├── ModelBased3d.java │ │ │ │ │ └── SparseCorrespondenceExtraction.java │ │ │ ├── segmentation │ │ │ │ ├── NucleiConfiguration.java │ │ │ │ ├── Nucleus.java │ │ │ │ ├── NucleusIdentification.java │ │ │ │ └── NucleusStructure.java │ │ │ └── threshold │ │ │ │ ├── ComponentProperties.java │ │ │ │ └── ConnectedComponent.java │ │ ├── segmentation │ │ │ ├── DOM.java │ │ │ ├── IntegralImage3d.java │ │ │ ├── InteractiveDoG.java │ │ │ ├── InteractiveIntegral.java │ │ │ └── SimplePeak.java │ │ ├── simulation │ │ │ └── SimulateBeadImage.java │ │ └── vis3d │ │ │ ├── PreviewRegistration.java │ │ │ ├── VisualizationFunctions.java │ │ │ ├── VisualizationSketchTikZ.java │ │ │ └── VisualizeBeads.java │ └── util │ │ └── TransformUtils.java └── spim │ ├── Threads.java │ ├── Version.java │ ├── fiji │ ├── datasetmanager │ │ ├── DHM.java │ │ ├── DHMMetaData.java │ │ ├── LightSheetZ1.java │ │ ├── LightSheetZ1MetaData.java │ │ ├── MicroManager.java │ │ ├── MultiViewDatasetDefinition.java │ │ ├── SlideBook6.java │ │ ├── SlideBook6Image.java │ │ ├── SlideBook6MetaData.java │ │ ├── StackList.java │ │ ├── StackListImageJ.java │ │ └── StackListLOCI.java │ ├── plugin │ │ ├── Apply_Transformation.java │ │ ├── Data_Explorer.java │ │ ├── Define_Bounding_Box.java │ │ ├── Define_Multi_View_Dataset.java │ │ ├── Display_View.java │ │ ├── Duplicate_Transformation.java │ │ ├── Image_Fusion.java │ │ ├── Interactive_Remove_Detections.java │ │ ├── Interest_Point_Detection.java │ │ ├── Interest_Point_Registration.java │ │ ├── Max_Project.java │ │ ├── Merge_Cluster_Jobs.java │ │ ├── Specify_Calibration.java │ │ ├── ThinOut_Detections.java │ │ ├── Toggle_Cluster_Options.java │ │ ├── Visualize_Detections.java │ │ ├── apply │ │ │ ├── ApplyParameters.java │ │ │ ├── BigDataViewerTransformationWindow.java │ │ │ └── ModelLink.java │ │ ├── cluster │ │ │ └── MergeClusterJobs.java │ │ ├── fusion │ │ │ └── Fusion.java │ │ ├── interestpointdetection │ │ │ ├── DifferenceOf.java │ │ │ ├── DifferenceOfGaussian.java │ │ │ ├── DifferenceOfMean.java │ │ │ └── InterestPointDetection.java │ │ ├── interestpointregistration │ │ │ └── InterestPointRegistration.java │ │ ├── queryXML │ │ │ ├── GenericLoadParseQueryXML.java │ │ │ └── LoadParseQueryXML.java │ │ ├── removedetections │ │ │ └── InteractiveProjections.java │ │ ├── resave │ │ │ ├── Generic_Resave_HDF5.java │ │ │ ├── PluginHelper.java │ │ │ ├── ProgressWriterIJ.java │ │ │ ├── Resave_HDF5.java │ │ │ └── Resave_TIFF.java │ │ ├── thinout │ │ │ ├── ChannelProcessThinOut.java │ │ │ ├── Histogram.java │ │ │ └── MouseListenerValue.java │ │ └── util │ │ │ ├── GUIHelper.java │ │ │ ├── GenericDialogAppender.java │ │ │ ├── MyMultiLineLabel.java │ │ │ └── OpenImg.java │ └── spimdata │ │ ├── EmptyEntity.java │ │ ├── NamePattern.java │ │ ├── SpimData2.java │ │ ├── SpimDataExample.java │ │ ├── ViewSetupUtils.java │ │ ├── XmlIoSpimData2.java │ │ ├── boundingbox │ │ ├── BoundingBox.java │ │ ├── BoundingBoxes.java │ │ ├── XmlIoBoundingBoxes.java │ │ └── XmlKeysBoundingBox.java │ │ ├── explorer │ │ ├── SelectedViewDescriptionListener.java │ │ ├── SimpleInfoBox.java │ │ ├── ViewSetupExplorer.java │ │ ├── ViewSetupExplorerInfoBox.java │ │ ├── ViewSetupExplorerPanel.java │ │ ├── ViewSetupTableModel.java │ │ ├── interestpoint │ │ │ ├── InterestPointExplorer.java │ │ │ ├── InterestPointExplorerPanel.java │ │ │ ├── InterestPointOverlay.java │ │ │ └── InterestPointTableModel.java │ │ ├── popup │ │ │ ├── ApplyTransformationPopup.java │ │ │ ├── BDVPopup.java │ │ │ ├── BakeManualTransformationPopup.java │ │ │ ├── BoundingBoxPopup.java │ │ │ ├── DetectInterestPointsPopup.java │ │ │ ├── DisplayViewPopup.java │ │ │ ├── FusionPopup.java │ │ │ ├── InterestPointsExplorerPopup.java │ │ │ ├── LabelPopUp.java │ │ │ ├── MaxProjectPopup.java │ │ │ ├── RegisterInterestPointsPopup.java │ │ │ ├── RegistrationExplorerPopup.java │ │ │ ├── RemoveDetectionsPopup.java │ │ │ ├── RemoveTransformationPopup.java │ │ │ ├── ReorientSamplePopup.java │ │ │ ├── ResavePopup.java │ │ │ ├── Separator.java │ │ │ ├── SpecifyCalibrationPopup.java │ │ │ ├── ViewExplorerSetable.java │ │ │ └── VisualizeDetectionsPopup.java │ │ ├── registration │ │ │ ├── RegistrationExplorer.java │ │ │ ├── RegistrationExplorerPanel.java │ │ │ └── RegistrationTableModel.java │ │ └── util │ │ │ └── ColorStream.java │ │ ├── imgloaders │ │ ├── AbstractImgFactoryImgLoader.java │ │ ├── AbstractImgLoader.java │ │ ├── CalibratedImg.java │ │ ├── Calibration.java │ │ ├── DHMImgLoader.java │ │ ├── LegacyDHMImgLoader.java │ │ ├── LegacyLightSheetZ1ImgLoader.java │ │ ├── LegacyMicroManagerImgLoader.java │ │ ├── LegacySlideBook6ImgLoader.java │ │ ├── LegacyStackImgLoader.java │ │ ├── LegacyStackImgLoaderIJ.java │ │ ├── LegacyStackImgLoaderLOCI.java │ │ ├── LightSheetZ1ImgLoader.java │ │ ├── MicroManagerImgLoader.java │ │ ├── MultipageTiffReader.java │ │ ├── NumberUtils.java │ │ ├── SlideBook6ImgLoader.java │ │ ├── StackImgLoader.java │ │ ├── StackImgLoaderIJ.java │ │ ├── StackImgLoaderLOCI.java │ │ ├── XmlIoDHMImgLoader.java │ │ ├── XmlIoLightSheetZ1ImgLoader.java │ │ ├── XmlIoMicroManagerImgLoader.java │ │ ├── XmlIoSlideBook6ImgLoader.java │ │ ├── XmlIoStackImgLoader.java │ │ ├── XmlIoStackImgLoaderIJ.java │ │ └── XmlIoStackImgLoaderLOCI.java │ │ └── interestpoints │ │ ├── CorrespondingInterestPoints.java │ │ ├── InterestPoint.java │ │ ├── InterestPointList.java │ │ ├── InterestPointValue.java │ │ ├── ViewInterestPointLists.java │ │ ├── ViewInterestPoints.java │ │ ├── XmlIoViewInterestPoints.java │ │ └── XmlKeysInterestPoints.java │ ├── process │ ├── cuda │ │ ├── Block.java │ │ ├── BlockGenerator.java │ │ ├── BlockGeneratorFixedSizePrecise.java │ │ ├── BlockGeneratorVariableSizePrecise.java │ │ ├── BlockGeneratorVariableSizeSimple.java │ │ ├── CUDADevice.java │ │ ├── CUDAFourierConvolution.java │ │ ├── CUDASeparableConvolution.java │ │ ├── CUDASeparableConvolutionFunctions.java │ │ ├── CUDAStandardFunctions.java │ │ ├── CUDATools.java │ │ └── NativeLibraryTools.java │ ├── fusion │ │ ├── FusionHelper.java │ │ ├── ImagePortion.java │ │ ├── boundingbox │ │ │ ├── AutomaticBoundingBox.java │ │ │ ├── AutomaticReorientation.java │ │ │ ├── BigDataViewerBoundingBox.java │ │ │ ├── BoundingBoxGUI.java │ │ │ ├── PreDefinedBoundingBox.java │ │ │ └── automatic │ │ │ │ └── MinFilterThreshold.java │ │ ├── deconvolution │ │ │ ├── AdjustInput.java │ │ │ ├── ChannelPSF.java │ │ │ ├── EfficientBayesianBased.java │ │ │ ├── ExtractPSF.java │ │ │ ├── FirstIteration.java │ │ │ ├── MVDeconFFT.java │ │ │ ├── MVDeconFFTThreads.java │ │ │ ├── MVDeconInput.java │ │ │ ├── MVDeconvolution.java │ │ │ ├── Mirror.java │ │ │ ├── ProcessForDeconvolution.java │ │ │ ├── TransformInput.java │ │ │ ├── TransformInputAndWeights.java │ │ │ ├── TransformWeights.java │ │ │ └── WeightNormalizer.java │ │ ├── export │ │ │ ├── AppendSpimData2.java │ │ │ ├── AppendSpimData2HDF5.java │ │ │ ├── DefaultImgTitler.java │ │ │ ├── DisplayImage.java │ │ │ ├── ExportSpimData2HDF5.java │ │ │ ├── ExportSpimData2TIFF.java │ │ │ ├── FixedNameImgTitler.java │ │ │ ├── ImgExport.java │ │ │ ├── ImgExportTitle.java │ │ │ ├── ImgTitler.java │ │ │ ├── Save3dTIFF.java │ │ │ └── XMLTIFFImgTitler.java │ │ ├── weightedavg │ │ │ ├── ProcessFusion.java │ │ │ ├── ProcessIndependent.java │ │ │ ├── ProcessIndependentPortion.java │ │ │ ├── ProcessParalell.java │ │ │ ├── ProcessParalellPortion.java │ │ │ ├── ProcessParalellPortionWeight.java │ │ │ ├── ProcessParalellPortionWeights.java │ │ │ ├── ProcessSequential.java │ │ │ ├── ProcessSequentialPortion.java │ │ │ ├── ProcessSequentialPortionWeight.java │ │ │ ├── ProcessSequentialPortionWeights.java │ │ │ └── WeightedAverageFusion.java │ │ └── weights │ │ │ ├── Blending.java │ │ │ ├── BlendingRealRandomAccess.java │ │ │ ├── ContentBased.java │ │ │ ├── NormalizingRandomAccess.java │ │ │ ├── NormalizingRandomAccessibleInterval.java │ │ │ ├── TransformedInterpolatedRealRandomAccess.java │ │ │ └── TransformedRealRandomAccessibleInterval.java │ ├── interestpointdetection │ │ ├── DifferenceOfGaussianCUDA.java │ │ ├── DifferenceOfGaussianNewPeakFinder.java │ │ ├── Downsample.java │ │ ├── Localization.java │ │ ├── ProcessDOG.java │ │ └── ProcessDOM.java │ └── interestpointregistration │ │ ├── ChannelProcess.java │ │ ├── Detection.java │ │ ├── GlobalOpt.java │ │ ├── MatchPointList.java │ │ ├── PairwiseMatch.java │ │ ├── RANSAC.java │ │ ├── RANSACParameters.java │ │ ├── TransformationModel.java │ │ ├── centerofmass │ │ ├── CenterOfMass.java │ │ └── CenterOfMassPairwise.java │ │ ├── geometricdescriptor │ │ ├── RGLDM.java │ │ ├── RGLDMMatcher.java │ │ ├── RGLDMPairwise.java │ │ └── RGLDMParameters.java │ │ ├── geometrichashing │ │ ├── GeometricHasher.java │ │ ├── GeometricHashing.java │ │ ├── GeometricHashingPairwise.java │ │ └── GeometricHashingParameters.java │ │ ├── icp │ │ ├── IterativeClosestPoint.java │ │ ├── IterativeClosestPointPairwise.java │ │ └── IterativeClosestPointParameters.java │ │ ├── optimizationtypes │ │ ├── AllToAllRegistration.java │ │ ├── AllToAllRegistrationWithRange.java │ │ ├── GlobalOptimizationSubset.java │ │ ├── GlobalOptimizationType.java │ │ ├── IndividualTimepointRegistration.java │ │ └── ReferenceTimepointRegistration.java │ │ └── registrationstatistics │ │ ├── GraphFrame.java │ │ ├── MouseListenerTimelapse.java │ │ ├── RegistrationStatistics.java │ │ ├── SelectTimepointEntry.java │ │ └── TimeLapseDisplay.java │ └── vecmath │ ├── AxisAngle4d.java │ ├── AxisAngle4f.java │ ├── Color3f.java │ ├── J3dHash.java │ ├── J3dI18N.java │ ├── Matrix3d.java │ ├── Matrix3f.java │ ├── Matrix4d.java │ ├── Matrix4f.java │ ├── Point3d.java │ ├── Point3f.java │ ├── Point3i.java │ ├── Point4d.java │ ├── Point4f.java │ ├── Quat4d.java │ ├── Quat4f.java │ ├── SingularMatrixException.java │ ├── Transform3D.java │ ├── Tuple3d.java │ ├── Tuple3f.java │ ├── Tuple3i.java │ ├── Tuple4d.java │ ├── Tuple4f.java │ ├── VecMathI18N.java │ ├── VecMathUtil.java │ ├── Vector3d.java │ ├── Vector3f.java │ ├── Vector4d.java │ └── Vector4f.java └── resources ├── ClassDiagramInterestPointRegistration.dia ├── LICENSE └── plugins.config /.github/build.sh: 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