├── .github ├── build.sh ├── setup.sh └── workflows │ ├── build-main.yml │ └── build-pr.yml ├── .gitignore ├── README.md ├── config.yml ├── images ├── Bars-G10-P15-stack-cropped.tif ├── BeadStack-crop.tif ├── CElegans-CY3-crop.tif ├── CElegans-CY3-crop.txt ├── PSF-Bars-stack-cropped-64.tif ├── PSF-Bars-stack-cropped.tif ├── PSF-BeadStack-crop-64.tif ├── PSF-BeadStack-crop.tif ├── bridge-odd.tif ├── bridge.tif └── lowresbridge.tif ├── matlab └── deconvolution │ ├── Donuts.asv │ ├── Donuts.m │ ├── donuts.md │ └── donuts.png ├── notebooks ├── Deconvolve.ipynb ├── General_EduRes_Heart_BloodVessels_0.jpg └── Tests.ipynb ├── ops-experiments-arrayfire ├── arrayfiresetup.md ├── arrayfiresetup.sh ├── native │ ├── CMakeLists.txt │ ├── FindOpenCL.cmake │ ├── arrayfiredecon │ │ ├── CMakeLists.txt │ │ ├── arrayfiredecon.cpp │ │ ├── arrayfiredecon.h │ │ └── cppbuild.sh │ ├── cppbuild.sh │ └── helloarrayfire │ │ ├── CMakeLists.txt │ │ └── helloarrayfire.cpp ├── pom.xml └── src │ └── main │ └── java │ └── net │ └── imagej │ └── ops │ └── experiments │ └── filter │ └── deconvolve │ ├── ArrayFireWrapper.java │ └── InteractiveArrayFireTests.java ├── ops-experiments-clij ├── README.md ├── license.txt ├── pom.xml └── src │ ├── main │ ├── java │ │ └── net │ │ │ └── haesleinhuepf │ │ │ └── clij │ │ │ └── customconvolutionplugin │ │ │ ├── Convolve.java │ │ │ ├── Deconvolve.java │ │ │ └── customConvolution.cl │ ├── macro │ │ ├── convolveDeconvolve.ijm │ │ ├── convolveDeconvolve3D.ijm │ │ └── convolveDeconvolveFly.ijm │ └── resources │ │ ├── PSF.tif │ │ └── plugins.config │ └── test │ └── java │ └── net │ └── haesleinhuepf │ └── clij │ └── customconvolutionplugin │ ├── DeconvolveBarsBenchmark.java │ ├── DeconvolveBenchmark.java │ ├── DeconvolveBenchmarkGauss.java │ └── DeconvolveBigImage.java ├── ops-experiments-common ├── pom.xml └── src │ ├── main │ └── java │ │ └── net │ │ └── imagej │ │ └── ops │ │ └── experiments │ │ ├── ConvertersUtility.java │ │ ├── ImageUtility.java │ │ ├── VisualizationUtility.java │ │ ├── deconvolution │ │ ├── NativeRichardsonLucy.java │ │ └── UnaryComputerNativeRichardsonLucy.java │ │ └── testImages │ │ ├── AbstractDeconvolutionPhantomData.java │ │ ├── AbstractDeconvolutionTestData.java │ │ ├── Bars.java │ │ ├── Bead.java │ │ ├── BeedPhantom.java │ │ ├── CElegans.java │ │ ├── DeconvolutionTestData.java │ │ └── HalfBead.java │ └── test │ └── java │ └── net │ └── imagej │ └── ops │ └── experiments │ ├── ConvertersTest.java │ └── OutOfBoundsCopyTest.java ├── ops-experiments-cuda ├── native │ ├── YacuDecu │ │ ├── CMakeLists.txt │ │ ├── Makefile │ │ ├── Makefile.windows │ │ ├── README.md │ │ ├── cppbuild.sh │ │ └── src │ │ │ ├── Makefile.windows │ │ │ ├── deconv.cu │ │ │ └── deconv.h │ ├── cppbuild.sh │ └── python │ │ └── source │ │ └── CMakeLists.txt ├── pom.xml └── src │ └── main │ └── java │ └── net │ └── imagej │ └── ops │ └── experiments │ └── filter │ └── deconvolve │ ├── AlgorithmMemory3D.java │ ├── BIGLabCElegansCudaDeconvolveTest.java │ ├── CudaDeconvolutionUtility.java │ ├── InteractiveCudaDeconvolveTest.java │ ├── InteractiveCudaTheoreticalTest.java │ ├── InteractiveSpecimentRIOtsuTesterTest.java │ ├── InteractiveSpecimentRefracticeIndexTesterTestRC.java │ ├── UnaryComputerYacuDecu.java │ ├── YacuDecuRichardsonLucyBatch.java │ ├── YacuDecuRichardsonLucyCommand.java │ ├── YacuDecuRichardsonLucyTheoreticalPSFCommand.java │ ├── YacuDecuRichardsonLucyWrapper.java │ └── YacuDecuSpecimenRIOtsuTester.java ├── ops-experiments-imglib2cache ├── pom.xml └── src │ └── main │ └── java │ └── net │ └── imagej │ └── ops │ └── experiments │ ├── GPUQueueMonitor.java │ ├── Imglib2CacheCudaDeconvolve.java │ ├── Imglib2CacheCudaDeconvolveTest.java │ ├── Imglib2CacheMultiGPUDeconvolveTest.java │ ├── RAICudaDeconvolveTest.java │ └── UnaryComputerYacuDecuWrapper.java ├── ops-experiments-main ├── .gitignore ├── .project ├── JavaCppNative │ ├── NativeLibrary.h │ ├── NativeLibrary.java │ ├── javacpp.jar │ ├── make.bat │ └── make.sh ├── images │ ├── Bars-G10-P15-stack-cropped.tif │ ├── PSF-Bars-stack-cropped.tif │ ├── bridge.tif │ └── lowresbridge.tif ├── native │ ├── MKLFFTW │ │ ├── CMakeLists.txt │ │ ├── cppbuild.sh │ │ └── src │ │ │ ├── MKLFFTW.cpp │ │ │ └── MKLFFTW.h │ ├── YacuDecu │ │ ├── CMakeLists.txt │ │ ├── Makefile │ │ ├── README.md │ │ ├── cppbuild.sh │ │ └── src │ │ │ ├── deconv.cu │ │ │ └── deconv.h │ └── cppbuild.sh ├── pom.xml ├── scripts │ └── DeconBenchMarkTheoreticalPSF.groovy └── src │ ├── main │ └── java │ │ └── net │ │ └── imagej │ │ └── ops │ │ └── experiments │ │ ├── fft │ │ ├── JFFTFloatRealForward2D.java │ │ └── JFFTFloatRealInverse2D.java │ │ ├── javacpp │ │ ├── NativeLibrary.h │ │ └── NativeLibrary.java │ │ └── phantoms │ │ └── BeadPhantom.java │ └── test │ └── java │ └── net │ └── imagej │ └── ops │ └── experiments │ ├── ConvertersUtilityTest.java │ ├── CudaUtility.java │ ├── HelloTest.java │ ├── LaunchImageJ.java │ ├── fft │ ├── CUFFTFloatRealForward2D.java │ ├── CUFFTFloatRealInverse2D.java │ ├── FFTBenchMark.java │ ├── FFTBenchMark3D.java │ ├── FFTWFloatRealForward2D.java │ ├── FFTWFloatRealInverse2D.java │ ├── InteractiveFFTTest.java │ ├── JFFTFloatComplexInverse2D.java │ ├── MKLFFTFloatRealForward2D.java │ └── ND4JFloatRealForward2D.java │ ├── filter │ ├── convolve │ │ ├── InteractiveConvolveTest.java │ │ └── JavaCPPConvolveOp.java │ └── deconvolve │ │ ├── InteractiveDeconvolveTest.java │ │ └── InteractiveDeconvolveTheoreticalTest.java │ ├── javacpp │ └── NativeLibraryTest.java │ └── kernel │ ├── GibsonLanni.java │ ├── InteractiveKernelTest.java │ └── WidefieldKernel.java ├── ops-experiments-mkl ├── mklsetup.sh ├── native │ ├── MKLFFTW │ │ ├── CMakeLists.txt │ │ ├── cppbuild.sh │ │ └── src │ │ │ ├── MKLFFTW.cpp │ │ │ └── MKLFFTW.h │ └── cppbuild.sh ├── pom.xml └── src │ └── main │ └── java │ └── net │ └── imagej │ └── ops │ └── experiments │ ├── fft │ ├── MKLFFTWFloatRealForward2D.java │ └── MKLFFTWFloatRealForward2DWrapper.java │ └── filter │ ├── convolve │ ├── MKLConvolve3DWrapper.java │ ├── MKLConvolveOp.java │ └── MKLConvolveWrapper.java │ └── deconvolve │ ├── InteractiveMKLDeconvolveTest.java │ ├── MKLRichardsonLucyWrapper.java │ ├── NativeDeconvolutionUtility.java │ └── UnaryComputerMKLDecon.java ├── ops-experiments-opencl ├── .vscode │ └── settings.json ├── build │ ├── Makefile │ ├── arrayfiredecon │ │ └── Makefile │ ├── helloarrayfire │ │ └── Makefile │ └── opencldeconv │ │ └── Makefile ├── ijscripts │ └── CLIJDecon.py ├── native │ ├── .vscode │ │ ├── c_cpp_properties.json │ │ └── settings.json │ ├── CMakeLists.txt │ ├── FindOpenCL.cmake │ ├── build │ │ ├── Makefile │ │ ├── arrayfiredecon │ │ │ └── Makefile │ │ ├── helloarrayfire │ │ │ └── Makefile │ │ └── opencldeconv │ │ │ └── Makefile │ ├── cppbuild.sh │ ├── lib │ │ ├── clFFT.dll │ │ ├── jniOpenCLWrapper.dll │ │ ├── jniOpenCLWrapper.lib │ │ ├── libclFFT.2.12.2.dylib │ │ ├── libclFFT.2.dylib │ │ ├── libclFFT.dylib │ │ ├── libclFFT.so │ │ ├── libclFFT.so.2 │ │ ├── libclFFT.so.2.12.2 │ │ ├── libopencldeconv.dylib │ │ ├── libopencldeconv.so │ │ └── opencldeconv.dll │ ├── opencldeconv │ │ ├── CL │ │ │ └── cl.h │ │ ├── CLIJFFTAlgorithms.md │ │ ├── CMakeLists.txt │ │ ├── clFFT.h │ │ ├── clFFT.version.h │ │ ├── cppbuild.sh │ │ ├── kernels.cl │ │ ├── multiply.cl │ │ ├── opencldeconv.cpp │ │ └── opencldeconv.h │ ├── opencldeconv_build │ │ ├── CL │ │ │ └── cl.hpp │ │ └── Makefile │ └── setenvironment.bat ├── openclsetup.md ├── openclsetup.sh ├── pom.xml └── src │ ├── main │ ├── java │ │ └── net │ │ │ ├── haesleinhuepf │ │ │ └── clijx │ │ │ │ └── plugins │ │ │ │ ├── DeconvolveFFT.java │ │ │ │ └── InteractiveDeconvolveFFTTest.java │ │ │ └── imagej │ │ │ └── ops │ │ │ └── experiments │ │ │ └── filter │ │ │ └── deconvolve │ │ │ ├── InteractiveOpenCLDeconvolveTest.java │ │ │ ├── InteractiveOpenCLFFTTest.java │ │ │ ├── OpenCLFFTUtility.java │ │ │ └── OpenCLWrapper.java │ └── jython │ │ └── CLIJDecon.py │ └── resources │ └── native │ └── lib │ ├── clFFT.dll │ ├── jniOpenCLWrapper.dll │ ├── jniOpenCLWrapper.lib │ ├── libclFFT.2.12.2.dylib │ ├── libclFFT.2.dylib │ ├── libclFFT.dylib │ ├── libclFFT.so │ ├── libclFFT.so.2 │ ├── libclFFT.so.2.12.2 │ ├── libopencldeconv.dylib │ ├── libopencldeconv.so │ └── opencldeconv.dll ├── ops-experiments-tensorflow ├── .project ├── images │ └── bars-25pct │ │ ├── actual.tif │ │ ├── data.tif │ │ └── kernel.tif ├── pom.xml └── src │ ├── main │ ├── java │ │ └── net │ │ │ └── imagej │ │ │ └── ops │ │ │ └── experiments │ │ │ └── filter │ │ │ └── deconvolve │ │ │ ├── Flowdec.java │ │ │ ├── FlowdecCli.java │ │ │ ├── FlowdecCommand.java │ │ │ ├── FlowdecGraph.java │ │ │ ├── FlowdecOp.java │ │ │ ├── FlowdecTask.java │ │ │ └── InteractiveTensorFlowDeconvolveTest.java │ └── resources │ │ └── tensorflow │ │ └── graphs │ │ ├── richardsonlucy-complex-1d │ │ ├── saved_model.pb │ │ └── saved_model.pbtxt │ │ ├── richardsonlucy-complex-2d │ │ ├── saved_model.pb │ │ └── saved_model.pbtxt │ │ └── 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