├── .gitattributes ├── .gitignore ├── App ├── MIRO_app.mlapp ├── MIRO_app.mlappinstall ├── MIRO_app.prj ├── MIRO_app_resources │ ├── icon_16.png │ ├── icon_24.png │ └── icon_48.png └── Test_Images │ ├── Raw_0010_actin.tif │ ├── Raw_0010_mitochondria.tif │ ├── Raw_0020_actin.tif │ ├── Raw_0020_mitochondria.tif │ ├── Raw_0050_actin.tif │ ├── Raw_0050_mitochondria.tif │ ├── Raw_0100_actin.tif │ └── Raw_0100_mitochondria.tif ├── Demo ├── Calibration_files │ ├── cmap.mat │ └── sCMOS_calibration.mat ├── GT │ └── GT.mat ├── MIRO_Demo.m ├── Raw_data │ ├── Raw_0010.mat │ ├── Raw_0020.mat │ ├── Raw_0050.mat │ └── Raw_0100.mat ├── calculate_PSNR.m └── calculate_SSIM.m ├── Figures ├── Image_Confocal.png ├── Image_SIM1.png ├── Image_SIM2.png └── Image_TIRF.png ├── Imdecorr ├── ResolutionFinder.m ├── apodImRect.m ├── getCorrcoef.m ├── getDcorr.m ├── getDcorrMax.m ├── getRadAvg.m ├── im2pol.m ├── linmap.m └── optional_files │ ├── clamp.m │ ├── getDcorrSect.m │ ├── getLocalDcorr.m │ └── loadData.m ├── LICENSE ├── MIRO.m ├── MIRO_functions ├── FPN Correction │ ├── MIRO_FPN_correction.m │ └── MIRO_Hotspot.m ├── Fast Wiener │ ├── MIRO_Fast_Wiener.m │ ├── MIRO_Fast_Wiener_Video.m │ ├── fast_wiener.mexa64 │ ├── fast_wiener.mexglx │ ├── fast_wiener.mexmaci │ ├── fast_wiener.mexmaci64 │ ├── fast_wiener.mexw32 │ ├── fast_wiener.mexw64 │ ├── fast_wiener_video.mexa64 │ ├── fast_wiener_video.mexglx │ ├── fast_wiener_video.mexmaci │ ├── fast_wiener_video.mexmaci64 │ ├── fast_wiener_video.mexw32 │ └── fast_wiener_video.mexw64 ├── MIRO_Default_Parameters.m ├── MIRO_main.m ├── MIRO_parse_inputs.m ├── Multiscale Wiener │ ├── MIRO_Aggregation.m │ ├── MIRO_Collaborative_Wiener_Initialization.m │ ├── MIRO_Collaborative_Wiener_dct.m │ ├── MIRO_Needle_match.m │ ├── MIRO_patch_3DFiltering.m │ ├── MIRO_patch_matching_and_processing.m │ └── MIRO_patch_matching_and_processing_mex.mexw64 ├── NLM │ ├── MIRO_image2vectors_double.c │ ├── MIRO_image2vectors_double.mexw64 │ ├── MIRO_nlm.m │ ├── MIRO_vectors_nlmeans_double.c │ ├── MIRO_vectors_nlmeans_double.mexw64 │ └── compile_MIRO_nlm.m └── Shearlet Shrinkage │ ├── MIRO_Hotspot2.m │ ├── MIRO_SLcheckFilterSizes.m │ ├── MIRO_SLgetShearletSystem2D.m │ ├── MIRO_SLprepareFilters2D.m │ ├── MIRO_Shearlet_thresholding.m │ ├── MIRO_Spectral_weighting.m │ └── MIRO_tophat.m ├── MIRO_install.m ├── MIRO_utils ├── Block_distance.m ├── Define_SearchWindow.m ├── Display_results.m ├── Display_results_percentage.m ├── Locate_blk.m ├── Pyramid.m ├── ReadTiff.m ├── Sigma_estimation.m ├── Spectral_filter.m ├── animated_comparison.m ├── cprintf.m ├── getSLsys.m ├── nrm.m ├── removePad.m ├── saveastiff.m └── textprogressbar.m ├── README.md └── ShearLab ├── MakeONFilter.m ├── MirrorFilt.m ├── SLcheckFilterSizes.m ├── SLdshear.m ├── SLfiltersToGPU2D.m ├── SLgetShearletIdxs2D.m ├── SLgetShearletSystem2D.m ├── SLgetShearlets2D.m ├── SLgetWedgeBandpassAndLowpassFilters2D.m ├── SLpadArray.m ├── SLprepareFilters2D.m ├── SLsheardec2D.m ├── SLshearrec2D.m 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