├── .gitattributes ├── .idea └── vcs.xml ├── Core ├── .flow ├── core.iml ├── resources │ └── About_NanoJ-Core.png └── src │ ├── nanoj │ ├── core │ │ └── java │ │ │ ├── Version.java │ │ │ ├── _Version_.java │ │ │ ├── aparapi │ │ │ ├── CLDevice.java │ │ │ ├── CLDevicesInfo.java │ │ │ ├── CLDevicesInfoTest.java │ │ │ ├── MandelSample.java │ │ │ └── NJKernel.java │ │ │ ├── array │ │ │ ├── ArrayCasting.java │ │ │ ├── ArrayInitialization.java │ │ │ ├── ArrayMath.java │ │ │ ├── ArrayTypeConversion.java │ │ │ ├── ImageStackToFromArray.java │ │ │ ├── ImageStackToFromArrayTest.java │ │ │ ├── MultidimensionalArrayIndexConversion.java │ │ │ └── MultidimensionalArrayIndexConversionTest.java │ │ │ ├── featureExtraction │ │ │ ├── BreakIntoBlocks.java │ │ │ ├── ExtractRois.java │ │ │ ├── ExtractSmallRegion.java │ │ │ ├── GenerateModelParticle.java │ │ │ ├── ImageMoments.java │ │ │ └── Peaks.java │ │ │ ├── gui │ │ │ ├── AbortNanoJExecution_.java │ │ │ ├── ApplyDriftCorrection.java │ │ │ ├── ChangeOpenCLDevice_.java │ │ │ ├── Debug_.java │ │ │ ├── DisplayOpenCLProperties_.java │ │ │ ├── DriftCorrection_.java │ │ │ ├── DriftEstimation_.java │ │ │ ├── LinksToManualAndPaper_.java │ │ │ ├── MTA_.java │ │ │ ├── Mandelbrot_.java │ │ │ ├── OpenCLPreferences_.java │ │ │ ├── ResetPreferences_.java │ │ │ ├── Version_.java │ │ │ ├── WhatsNew_.java │ │ │ ├── _BaseDialog_.java │ │ │ ├── _BaseTestWithPath_.java │ │ │ ├── analysis │ │ │ │ └── CalculateFRC_.java │ │ │ ├── benchmark │ │ │ │ └── ConvolutionSpeed_.java │ │ │ ├── localisation │ │ │ │ ├── DualChannelNearestNeighboursAnalysis_.java │ │ │ │ ├── FluorophoreRateExtraction_.java │ │ │ │ └── NearestNeighboursAnalysis_.java │ │ │ ├── registration │ │ │ │ ├── ChannelRealignment_Apply_.java │ │ │ │ └── ChannelRealignment_Estimate_.java │ │ │ └── tools │ │ │ │ ├── featureExtraction │ │ │ │ └── ExtractROIs_.java │ │ │ │ ├── filtering │ │ │ │ ├── convolution │ │ │ │ │ ├── DoG_.java │ │ │ │ │ ├── ExtendedLaplacian_.java │ │ │ │ │ ├── GradientX_.java │ │ │ │ │ ├── GradientY_.java │ │ │ │ │ ├── LoG_.java │ │ │ │ │ └── _BaseConvolutionDialog_.java │ │ │ │ ├── convolution3D │ │ │ │ │ ├── Smooth_.java │ │ │ │ │ └── _BaseDialog_.java │ │ │ │ └── wavelets │ │ │ │ │ └── A_trous_filter.java │ │ │ │ ├── io │ │ │ │ ├── CalculateChecksum_.java │ │ │ │ ├── ConvertImageSequencesIntoNJI_.java │ │ │ │ ├── ConvertResultTableFilesIntoNJT_.java │ │ │ │ ├── OpenImageFormatAsImageSequence_.java │ │ │ │ ├── OpenNanoJStack_.java │ │ │ │ ├── OpenNanoJTable_.java │ │ │ │ ├── SaveResultsTableAsNJT_.java │ │ │ │ ├── SaveStackAsNJB_.java │ │ │ │ ├── SaveStackAsNJI_.java │ │ │ │ └── SetCompression_.java │ │ │ │ ├── projections │ │ │ │ └── Projections2D_.java │ │ │ │ └── transform │ │ │ │ ├── CrossCorrelationMap_.java │ │ │ │ ├── DecreaseImageSize_.java │ │ │ │ ├── FHT_.java │ │ │ │ ├── FilamentAnalysis_.java │ │ │ │ ├── IncreaseImageSize_.java │ │ │ │ ├── NormalizedCrossCorrelationMap_.java │ │ │ │ ├── NormalizedRotationAndCrossCorrelationMap_.java │ │ │ │ ├── PolarTransform_.java │ │ │ │ ├── Rotate_.java │ │ │ │ └── Translate_.java │ │ │ ├── image │ │ │ ├── analysis │ │ │ │ ├── CalculateImageStatistics.java │ │ │ │ ├── CalculateNoiseAndBackground.java │ │ │ │ └── FRC.java │ │ │ ├── binary │ │ │ │ └── SkeletonAnalysis.java │ │ │ ├── calculator │ │ │ │ ├── FloatProcessorCalculator.java │ │ │ │ └── ImageCalculator.java │ │ │ ├── drift │ │ │ │ └── EstimateShiftAndTilt.java │ │ │ ├── filtering │ │ │ │ ├── ConvolutionKernels.java │ │ │ │ ├── ConvolutionKernelsTest.java │ │ │ │ └── Convolve.java │ │ │ ├── handeling │ │ │ │ ├── ImageConcatenator.java │ │ │ │ ├── LateralJoinStackBlocks.java │ │ │ │ └── ReshuffleDimensions.java │ │ │ ├── registration │ │ │ │ └── CrossCorrelationElastic.java │ │ │ ├── rendering │ │ │ │ ├── FullFrameGaussRendering.java │ │ │ │ └── SubPixelGaussianRendering.java │ │ │ └── transform │ │ │ │ ├── CrossCorrelationMap.java │ │ │ │ ├── NJ_FHT.java │ │ │ │ ├── NormalizedCrossCorrelationMap.java │ │ │ │ ├── NormalizedRotationAndCrossCorrelationMap.java │ │ │ │ ├── NormalizedRotationCorrelationMap.java │ │ │ │ ├── PolarTransform.java │ │ │ │ ├── ResizeImage.java │ │ │ │ ├── TranslateOrRotateImage.java │ │ │ │ └── ZeroFillWithInterpolation.java │ │ │ ├── imagej │ │ │ ├── FilesAndFoldersTools.java │ │ │ ├── ImagePlusTools.java │ │ │ ├── NJImagePlus.java │ │ │ ├── PrefsClassHandler.java │ │ │ └── ResultsTableTools.java │ │ │ ├── io │ │ │ ├── IOTools.java │ │ │ ├── LoadNanoJTable.java │ │ │ ├── OpenNanoJDataset.java │ │ │ ├── SaveLoadParticlesHolder.java │ │ │ ├── SaveNanoJTable.java │ │ │ ├── ThreadedImageSave.java │ │ │ ├── ThreadedPartitionData.java │ │ │ └── zip │ │ │ │ ├── OpenFileWithinZip.java │ │ │ │ ├── ParseFileNamesInZip.java │ │ │ │ ├── SaveFileInZip.java │ │ │ │ ├── filesInZipTypes │ │ │ │ ├── TextFileInZip.java │ │ │ │ ├── TiffFileInZip.java │ │ │ │ └── _BaseFileInZip_.java │ │ │ │ ├── imageInBlocks │ │ │ │ ├── OpenImageFromBlocksInZip.java │ │ │ │ └── SaveImageByBlocksInZip.java │ │ │ │ ├── threadedSave │ │ │ │ ├── ThreadedImageSaveByBlocksInZip.java │ │ │ │ ├── ThreadedImageSaveInZip.java │ │ │ │ └── _BaseThreadedImageSave_.java │ │ │ │ └── virtualStacks │ │ │ │ ├── BaseVirtualStack.java │ │ │ │ ├── BlocksVirtualStack.java │ │ │ │ ├── FramesFromBlocksVirtualStack.java │ │ │ │ └── FullFramesVirtualStack.java │ │ │ ├── localisation │ │ │ ├── particlesHandling │ │ │ │ ├── ParticlesHolder.java │ │ │ │ ├── ParticlesHolderTest.java │ │ │ │ └── SimulateStackWithParticles.java │ │ │ └── peakDetection │ │ │ │ ├── LocalMaximaDetector.java │ │ │ │ ├── MaximumFinder.java │ │ │ │ ├── PeakFinderTest.java │ │ │ │ ├── RoiTools.java │ │ │ │ ├── SmoothPeakFinder.java │ │ │ │ └── SmoothPeakFinderTest.java │ │ │ ├── optimizers │ │ │ └── particleSwarm │ │ │ │ ├── PSOConstants.java │ │ │ │ ├── PSOOptimizer.java │ │ │ │ └── PSOParticle.java │ │ │ ├── projections │ │ │ ├── Projections2D.java │ │ │ └── Projections3D.java │ │ │ ├── threading │ │ │ └── NanoJThreadExecutor.java │ │ │ └── tools │ │ │ ├── Colors.java │ │ │ ├── DateTime.java │ │ │ ├── DontShowAgainDialog.java │ │ │ ├── Exceptions.java │ │ │ ├── JythonLauncher_.java │ │ │ ├── Log.java │ │ │ ├── MapTools.java │ │ │ ├── Memory.java │ │ │ ├── NJ_LUT.java │ │ │ ├── Options.java │ │ │ ├── Prefs.java │ │ │ ├── download │ │ │ └── ThreadedDownload.java │ │ │ ├── fit │ │ │ ├── EllipsoidFit.java │ │ │ ├── GaussianEllipsoidFitWithAngle2D.java │ │ │ └── _BaseFit2D_.java │ │ │ └── math │ │ │ ├── CubicSolver.java │ │ │ ├── LogFactorial.java │ │ │ ├── NthRoot.java │ │ │ ├── Randomizer.java │ │ │ └── RandomizerTest.java │ ├── core2 │ │ ├── NanoJCL.java │ │ ├── NanoJCrossCorrelation.java │ │ ├── NanoJFHT.java │ │ ├── NanoJImageStackArrayConvertion.java │ │ ├── NanoJPrefs.java │ │ ├── NanoJProfiler.java │ │ ├── NanoJRandomNoise.java │ │ ├── NanoJThreadExecutor.java │ │ └── NanoJUsageTracker.java │ └── kernels │ │ ├── Kernel_BasePSO.java │ │ ├── Kernel_CalculatePeaks.java │ │ ├── Kernel_LineAndOrientationFilterTransform.java │ │ ├── Kernel_LocalSimilarity.java │ │ ├── Kernel_NearestNeighbour.java │ │ ├── Kernel_PointsToMap.java │ │ └── Kernel_VoronoiImage.java │ └── plugins.config ├── GNU_GPL_LICENSE.txt ├── NanoJ-Core_LICENSE.txt ├── README.md └── Updater ├── .flow ├── resources ├── NanoJ-Orange.lut ├── SQUIRREL-Errors.lut ├── SQUIRREL-FRC.lut ├── aparapi_x86.dll ├── aparapi_x86_64.dll ├── calculating.gif ├── libaparapi_x86.so ├── libaparapi_x86_64.dylib └── libaparapi_x86_64.so ├── src ├── nanoj │ └── updater │ │ └── java │ │ ├── InstallNanoJDependencies.java │ │ ├── LibraryPath.java │ │ ├── MTA.java │ │ ├── NativeTools.java │ │ └── Path.java └── plugins.config └── updater.iml /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HenriquesLab/NanoJ-Core/HEAD/.gitattributes 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