├── LICENSE ├── README.md ├── SIMnoise code ├── SIMdata.m ├── SIMdata_reformat_omx.m ├── SIMdata_reformat_zeiss.m ├── SIMdeconvolution.m ├── SIMpatterns.m ├── SIMreconstruction.m ├── data │ ├── OMXdatafiles │ │ └── OMX_data_dir_download_data.txt │ └── Zeissdatafiles │ │ └── Zeiss_data_dir_download_data.txt ├── helperfunctions │ ├── add_comfortnoise.m │ ├── blend_stack.m │ ├── blur_extend.m │ ├── check_patternestimaterepeats.m │ ├── check_patternestimaterepeats_script.m │ ├── colorMatchFcn.m │ ├── complexparity.m │ ├── correct_gain.m │ ├── correct_globalphase.m │ ├── cztfunc.m │ ├── do_OTFbenchmark.m │ ├── do_OTFmasking3D.m │ ├── do_RichardsonLucy.m │ ├── do_axialprojection.m │ ├── do_binosplit.m │ ├── do_filtering.m │ ├── do_inspectorders.m │ ├── do_modulationcheck.m │ ├── do_ordershift.m │ ├── do_pixel_blurring.m │ ├── do_poissoncheck.m │ ├── do_shiftOTFmasking.m │ ├── do_upsample.m │ ├── doallscripts.m │ ├── estimate_patternphases.m │ ├── find_illumination_patterns.m │ ├── find_notchpars.m │ ├── get_apodization.m │ ├── get_apodization_v0.m │ ├── get_calibrationOTF.m │ ├── get_field_matrix.m │ ├── get_imagecorrelationmatrix.m │ ├── get_maxmerit.m │ ├── get_modelOTF.m │ ├── get_modelbasedSSNR.m │ ├── get_normalization.m │ ├── get_notchMTFmerit.m │ ├── get_orders.m │ ├── get_orderstrengths_overlap.m │ ├── get_otf3d.m │ ├── get_preWienerSIMrecon.m │ ├── get_psf.m │ ├── get_pupil_matrix.m │ ├── get_reconfuncs.m │ ├── get_reconfuncs_v0.m │ ├── get_rimismatchpars.m │ ├── get_shiftnotch.m │ ├── get_simnoisevariance.m │ ├── get_simotf.m │ ├── get_throughfocusotf.m │ ├── get_vectormodelOTF.m │ ├── get_widefield.m │ ├── get_widefieldSSNR.m │ ├── get_wiener_flatnoise.m │ ├── get_wiener_stateofart.m │ ├── get_wiener_truewiener.m │ ├── get_window2D.m │ ├── get_zernikefunctions.m │ ├── otsuthreshold.m │ ├── phasemeritfunc.m │ ├── polyfitweighted2.m │ ├── prechirpz.m │ ├── radialavgmat.m │ ├── resample_calibrationOTF.m │ ├── show_reconstructions.m │ ├── spectrumRGB.m │ └── update_qvector.m ├── simnoise.m └── simnoise_zeiss.m ├── experiment DMD SIM ├── bp_filter.m ├── bp_filter_new.m ├── cztfunc.m ├── find_DMDpattern.m ├── findgrid_nc2_square.m ├── finemax.m ├── ft2.m ├── generate_illum_patterns.m ├── get_field_matrix.m ├── get_otf.m ├── get_psfs.m ├── ift2.m ├── myshift2d.m ├── prechirpz.m ├── reconstruction_PIFP.m ├── sanity_check.m ├── triangle_apodization.m └── unit.m ├── makefiguresmovies ├── frcbis.m ├── get_frcvals.m ├── get_noisefraction.m ├── isect.m ├── make_figure1_noisepropagation.m ├── make_figure2_noisecontrolSIM.m ├── make_figure3_tradeoffSIM.m ├── make_figure4_3DSIMnoise.m ├── make_figure4andsfigure6_3DSIMnoise.m ├── make_figure5_RLdeconvolution.m ├── make_figure5_deconvolution.m ├── make_sfigure10_beadlayer.m ├── make_sfigure14_MCNRthroughfocus.m ├── make_sfigure16_MCNRthroughfocus.m ├── make_sfigure1_overview.m ├── make_sfigure2_testslide.m ├── make_sfigure4_tradeoffSIM.m ├── make_sfigure5_synaptonemal.m ├── make_sfigure6_signallevel3D.m ├── make_sfigure7_signallevel3D.m ├── make_sfigure7_ssnr.m ├── make_sfigure8_mtfs_noise.m ├── make_sfigure8_ssnr.m ├── make_sfigure9_beadlayer.m ├── make_sfigure9_mtfs_noise.m ├── make_sfigures10and11_cell3Dcoulor.m ├── make_sfigures11and12_cell3Dcoulor.m ├── make_smovie1_regularizationrun.m ├── make_smovie2_noisecontrolSIM.m ├── make_smovie9_livecell.m ├── make_smovie9andsfigure13and14_livecell.m ├── make_smovies3to6_throughfocusSIM.m └── make_smovies7and8_throughfocuscolorSIM.m └── readme file with SIM noise Matlab code v1.0.pdf /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/README.md -------------------------------------------------------------------------------- /SIMnoise code/SIMdata.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/SIMdata.m -------------------------------------------------------------------------------- /SIMnoise code/SIMdata_reformat_omx.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/SIMdata_reformat_omx.m -------------------------------------------------------------------------------- /SIMnoise code/SIMdata_reformat_zeiss.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/SIMdata_reformat_zeiss.m -------------------------------------------------------------------------------- /SIMnoise code/SIMdeconvolution.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/SIMdeconvolution.m -------------------------------------------------------------------------------- /SIMnoise code/SIMpatterns.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/SIMpatterns.m -------------------------------------------------------------------------------- /SIMnoise code/SIMreconstruction.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/SIMreconstruction.m -------------------------------------------------------------------------------- /SIMnoise code/data/OMXdatafiles/OMX_data_dir_download_data.txt: -------------------------------------------------------------------------------- 1 | Download example data from: https://doi.org/10.4121/14428124 -------------------------------------------------------------------------------- /SIMnoise code/data/Zeissdatafiles/Zeiss_data_dir_download_data.txt: -------------------------------------------------------------------------------- 1 | Download example data from: https://doi.org/10.4121/14428124 -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/add_comfortnoise.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/add_comfortnoise.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/blend_stack.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/blend_stack.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/blur_extend.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/blur_extend.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/check_patternestimaterepeats.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/check_patternestimaterepeats.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/check_patternestimaterepeats_script.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/check_patternestimaterepeats_script.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/colorMatchFcn.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/colorMatchFcn.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/complexparity.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/complexparity.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/correct_gain.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/correct_gain.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/correct_globalphase.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/correct_globalphase.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/cztfunc.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/cztfunc.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/do_OTFbenchmark.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/do_OTFbenchmark.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/do_OTFmasking3D.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/do_OTFmasking3D.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/do_RichardsonLucy.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/do_RichardsonLucy.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/do_axialprojection.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/do_axialprojection.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/do_binosplit.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/do_binosplit.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/do_filtering.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/do_filtering.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/do_inspectorders.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/do_inspectorders.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/do_modulationcheck.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/do_modulationcheck.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/do_ordershift.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/do_ordershift.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/do_pixel_blurring.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/do_pixel_blurring.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/do_poissoncheck.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/do_poissoncheck.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/do_shiftOTFmasking.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/do_shiftOTFmasking.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/do_upsample.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/do_upsample.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/doallscripts.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/doallscripts.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/estimate_patternphases.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/estimate_patternphases.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/find_illumination_patterns.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/find_illumination_patterns.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/find_notchpars.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/find_notchpars.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_apodization.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_apodization.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_apodization_v0.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_apodization_v0.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_calibrationOTF.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_calibrationOTF.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_field_matrix.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_field_matrix.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_imagecorrelationmatrix.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_imagecorrelationmatrix.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_maxmerit.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_maxmerit.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_modelOTF.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_modelOTF.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_modelbasedSSNR.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_modelbasedSSNR.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_normalization.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_normalization.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_notchMTFmerit.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_notchMTFmerit.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_orders.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_orders.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_orderstrengths_overlap.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_orderstrengths_overlap.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_otf3d.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_otf3d.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_preWienerSIMrecon.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_preWienerSIMrecon.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_psf.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_psf.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_pupil_matrix.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_pupil_matrix.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_reconfuncs.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_reconfuncs.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_reconfuncs_v0.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_reconfuncs_v0.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_rimismatchpars.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_rimismatchpars.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_shiftnotch.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_shiftnotch.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_simnoisevariance.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_simnoisevariance.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_simotf.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_simotf.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_throughfocusotf.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_throughfocusotf.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_vectormodelOTF.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_vectormodelOTF.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_widefield.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_widefield.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_widefieldSSNR.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_widefieldSSNR.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_wiener_flatnoise.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_wiener_flatnoise.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_wiener_stateofart.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_wiener_stateofart.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_wiener_truewiener.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_wiener_truewiener.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_window2D.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_window2D.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/get_zernikefunctions.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/get_zernikefunctions.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/otsuthreshold.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/otsuthreshold.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/phasemeritfunc.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/phasemeritfunc.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/polyfitweighted2.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/polyfitweighted2.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/prechirpz.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/prechirpz.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/radialavgmat.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/radialavgmat.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/resample_calibrationOTF.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/resample_calibrationOTF.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/show_reconstructions.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/show_reconstructions.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/spectrumRGB.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/spectrumRGB.m -------------------------------------------------------------------------------- /SIMnoise code/helperfunctions/update_qvector.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/helperfunctions/update_qvector.m -------------------------------------------------------------------------------- /SIMnoise code/simnoise.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/simnoise.m -------------------------------------------------------------------------------- /SIMnoise code/simnoise_zeiss.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/SIMnoise code/simnoise_zeiss.m -------------------------------------------------------------------------------- /experiment DMD SIM/bp_filter.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/bp_filter.m -------------------------------------------------------------------------------- /experiment DMD SIM/bp_filter_new.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/bp_filter_new.m -------------------------------------------------------------------------------- /experiment DMD SIM/cztfunc.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/cztfunc.m -------------------------------------------------------------------------------- /experiment DMD SIM/find_DMDpattern.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/find_DMDpattern.m -------------------------------------------------------------------------------- /experiment DMD SIM/findgrid_nc2_square.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/findgrid_nc2_square.m -------------------------------------------------------------------------------- /experiment DMD SIM/finemax.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/finemax.m -------------------------------------------------------------------------------- /experiment DMD SIM/ft2.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/ft2.m -------------------------------------------------------------------------------- /experiment DMD SIM/generate_illum_patterns.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/generate_illum_patterns.m -------------------------------------------------------------------------------- /experiment DMD SIM/get_field_matrix.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/get_field_matrix.m -------------------------------------------------------------------------------- /experiment DMD SIM/get_otf.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/get_otf.m -------------------------------------------------------------------------------- /experiment DMD SIM/get_psfs.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/get_psfs.m -------------------------------------------------------------------------------- /experiment DMD SIM/ift2.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/ift2.m -------------------------------------------------------------------------------- /experiment DMD SIM/myshift2d.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/myshift2d.m -------------------------------------------------------------------------------- /experiment DMD SIM/prechirpz.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/prechirpz.m -------------------------------------------------------------------------------- /experiment DMD SIM/reconstruction_PIFP.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/reconstruction_PIFP.m -------------------------------------------------------------------------------- /experiment DMD SIM/sanity_check.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/sanity_check.m -------------------------------------------------------------------------------- /experiment DMD SIM/triangle_apodization.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/triangle_apodization.m -------------------------------------------------------------------------------- /experiment DMD SIM/unit.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/experiment DMD SIM/unit.m -------------------------------------------------------------------------------- /makefiguresmovies/frcbis.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/frcbis.m -------------------------------------------------------------------------------- /makefiguresmovies/get_frcvals.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/get_frcvals.m -------------------------------------------------------------------------------- /makefiguresmovies/get_noisefraction.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/get_noisefraction.m -------------------------------------------------------------------------------- /makefiguresmovies/isect.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/isect.m -------------------------------------------------------------------------------- /makefiguresmovies/make_figure1_noisepropagation.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_figure1_noisepropagation.m -------------------------------------------------------------------------------- /makefiguresmovies/make_figure2_noisecontrolSIM.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_figure2_noisecontrolSIM.m -------------------------------------------------------------------------------- /makefiguresmovies/make_figure3_tradeoffSIM.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_figure3_tradeoffSIM.m -------------------------------------------------------------------------------- /makefiguresmovies/make_figure4_3DSIMnoise.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_figure4_3DSIMnoise.m -------------------------------------------------------------------------------- /makefiguresmovies/make_figure4andsfigure6_3DSIMnoise.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_figure4andsfigure6_3DSIMnoise.m -------------------------------------------------------------------------------- /makefiguresmovies/make_figure5_RLdeconvolution.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_figure5_RLdeconvolution.m -------------------------------------------------------------------------------- /makefiguresmovies/make_figure5_deconvolution.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_figure5_deconvolution.m -------------------------------------------------------------------------------- /makefiguresmovies/make_sfigure10_beadlayer.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_sfigure10_beadlayer.m -------------------------------------------------------------------------------- /makefiguresmovies/make_sfigure14_MCNRthroughfocus.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_sfigure14_MCNRthroughfocus.m -------------------------------------------------------------------------------- /makefiguresmovies/make_sfigure16_MCNRthroughfocus.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_sfigure16_MCNRthroughfocus.m -------------------------------------------------------------------------------- /makefiguresmovies/make_sfigure1_overview.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_sfigure1_overview.m -------------------------------------------------------------------------------- /makefiguresmovies/make_sfigure2_testslide.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_sfigure2_testslide.m -------------------------------------------------------------------------------- /makefiguresmovies/make_sfigure4_tradeoffSIM.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_sfigure4_tradeoffSIM.m -------------------------------------------------------------------------------- /makefiguresmovies/make_sfigure5_synaptonemal.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_sfigure5_synaptonemal.m -------------------------------------------------------------------------------- /makefiguresmovies/make_sfigure6_signallevel3D.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_sfigure6_signallevel3D.m -------------------------------------------------------------------------------- /makefiguresmovies/make_sfigure7_signallevel3D.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_sfigure7_signallevel3D.m -------------------------------------------------------------------------------- /makefiguresmovies/make_sfigure7_ssnr.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_sfigure7_ssnr.m -------------------------------------------------------------------------------- /makefiguresmovies/make_sfigure8_mtfs_noise.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_sfigure8_mtfs_noise.m -------------------------------------------------------------------------------- /makefiguresmovies/make_sfigure8_ssnr.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_sfigure8_ssnr.m -------------------------------------------------------------------------------- /makefiguresmovies/make_sfigure9_beadlayer.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_sfigure9_beadlayer.m -------------------------------------------------------------------------------- /makefiguresmovies/make_sfigure9_mtfs_noise.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_sfigure9_mtfs_noise.m -------------------------------------------------------------------------------- /makefiguresmovies/make_sfigures10and11_cell3Dcoulor.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_sfigures10and11_cell3Dcoulor.m -------------------------------------------------------------------------------- /makefiguresmovies/make_sfigures11and12_cell3Dcoulor.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_sfigures11and12_cell3Dcoulor.m -------------------------------------------------------------------------------- /makefiguresmovies/make_smovie1_regularizationrun.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_smovie1_regularizationrun.m -------------------------------------------------------------------------------- /makefiguresmovies/make_smovie2_noisecontrolSIM.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_smovie2_noisecontrolSIM.m -------------------------------------------------------------------------------- /makefiguresmovies/make_smovie9_livecell.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_smovie9_livecell.m -------------------------------------------------------------------------------- /makefiguresmovies/make_smovie9andsfigure13and14_livecell.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_smovie9andsfigure13and14_livecell.m -------------------------------------------------------------------------------- /makefiguresmovies/make_smovies3to6_throughfocusSIM.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_smovies3to6_throughfocusSIM.m -------------------------------------------------------------------------------- /makefiguresmovies/make_smovies7and8_throughfocuscolorSIM.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/makefiguresmovies/make_smovies7and8_throughfocuscolorSIM.m -------------------------------------------------------------------------------- /readme file with SIM noise Matlab code v1.0.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qnano/simnoise/HEAD/readme file with SIM noise Matlab code v1.0.pdf --------------------------------------------------------------------------------