├── .gitignore ├── README.md ├── SIMToolbox1.10_MATLAB ├── ReadMe.txt ├── SIMToolbox.m ├── config.m ├── license │ └── COPYING.txt ├── process.m ├── setEstimatePatterns.m ├── setFindPeaks.m ├── spotfinder_method_calibration.m ├── spotfinder_method_spotfinder.m └── utils │ ├── apodize │ ├── apodize_butterworth.m │ ├── apodize_circular.m │ ├── apodize_cosbell.m │ ├── apodize_gauss.m │ ├── apodize_lukosz.m │ ├── apodize_none.m │ ├── apodize_standard.m │ ├── apodize_triangle.m │ └── getapodizationnames.m │ ├── calibration │ ├── cal2Destim.cpp │ ├── cal2Destim.mexw32 │ ├── calconfig.m │ ├── calhomolin.m │ ├── calhomorad.m │ ├── cali2w.m │ ├── calload.m │ ├── calloadgdf.m │ ├── calprocess.m │ ├── calsave.m │ ├── calw2i.m │ ├── cart2sq.m │ ├── corners_detect.m │ ├── markers_check.m │ ├── markers_detect.m │ ├── markers_sort.m │ └── ptdist.m │ ├── image │ ├── fspecialseparable.m │ ├── imfilterseparable.m │ ├── imgadjust.m │ ├── imgclipval.m │ ├── imgflatfield.m │ ├── imgradprof.m │ └── imgrmpadding.m │ ├── io │ ├── cfgload.m │ ├── cfgsave.m │ ├── dimload.m │ ├── extractPathAndFilename.m │ ├── fileparts_dir.m │ ├── fileparts_name.m │ ├── fileparts_nameext.m │ ├── fixresname.m │ ├── imgdirinfo.m │ ├── imginfoinit.m │ ├── imgload.m │ ├── imgsave16.m │ ├── imgsave32.m │ ├── imgzload.m │ ├── iq2getinfo.m │ ├── iq2parse.m │ ├── isfile.m │ ├── loadtif.m │ └── tiffnumpg.m │ ├── misc │ ├── fftInterpolate.m │ ├── lmfit1DgaussXSAO.cpp │ ├── lmfit1DgaussXSAO.mexw32 │ ├── lmfit1DgaussXSAO.mexw64 │ ├── lmfit2DgaussXYSAO.cpp │ ├── lmfit2DgaussXYSAO.mexw32 │ ├── lmfit2DgaussXYSAO.mexw64 │ ├── lmmin │ │ ├── lm_eval.c │ │ ├── lmmin.c │ │ └── lmmin.h │ ├── locmax1d.m │ ├── m2c.m │ ├── printerror.m │ ├── rmfields.m │ ├── sigmoid.m │ ├── sizeof.m │ ├── structcat.m │ ├── timestamp.m │ └── whichcamera.m │ ├── patterns │ ├── ptrn2camera.m │ ├── ptrnchecklines.m │ ├── ptrnclose.m │ ├── ptrndirinfo.m │ ├── ptrngetimagenames.m │ ├── ptrngetnumro.m │ ├── ptrngetnumseq.m │ ├── ptrngetro.m │ ├── ptrnload.m │ ├── ptrnmaskprecompute.m │ └── ptrnopen.m │ ├── prepareData │ ├── gen_descfile.m │ ├── gen_ptrnest.m │ ├── gen_repfile.m │ ├── gen_repz.m │ ├── get_ptrnimagenames.m │ └── ro_lines.m │ ├── sim-msm │ ├── genMasks.m │ └── mapsim.m │ ├── sim-sr │ ├── sim_addOTF.m │ ├── sim_combine.m │ ├── sim_extract.m │ ├── sim_findpeaks.m │ ├── sim_findpeaksassign.m │ ├── sim_findpeaksloadimage.m │ ├── sim_matchspectra.m │ └── sim_shiftspectra.m │ ├── sim-vsm │ ├── getvsmnames.m │ ├── seqcfhomodyne.m │ ├── seqcfmaskonly.m │ ├── seqcfmaxmin.m │ ├── seqcfmaxmin2av.m │ ├── seqcfscaledsub.m │ ├── seqcfscaledsub1px.m │ ├── seqcfscaledsubbeta.m │ ├── seqopav.m │ ├── seqopmax.m │ ├── seqopmin.m │ ├── seqopsum.m │ ├── seqopsummaskoff.m │ ├── seqopsummaskon.m │ ├── seqsubseq.m │ └── seqwf.m │ ├── sim │ ├── runseqflatfield.m │ ├── seq2subseq.m │ ├── seqblure.m │ ├── seqfft2.m │ ├── seqflatfield.m │ ├── seqifft2.m │ ├── seqload.m │ ├── seqpadsmooth.m │ ├── seqremovemean.m │ ├── seqrewind.m │ └── seqstriperemoval.m │ ├── spotfinder │ ├── detector_locmax.m │ ├── estimator_lsq_fitquadric.m │ ├── estimator_lsq_gradintersect.m │ ├── estimator_none.m │ ├── filter_dao.m │ ├── filter_daoint.m │ ├── filter_diffav.m │ ├── filter_dog.m │ ├── filter_dogint.m │ ├── filter_gauss.m │ ├── filter_gaussint.m │ ├── filter_none.m │ ├── filter_wavelet.m │ ├── mex │ │ ├── boxmustd.cpp │ │ ├── boxmustd.mexw32 │ │ ├── boxmustd.mexw64 │ │ ├── circfilter.cpp │ │ ├── circfilter.mexw32 │ │ ├── circfilter.mexw64 │ │ ├── findlocmax2d.cpp │ │ ├── findlocmax2d.mexw32 │ │ ├── findlocmax2d.mexw64 │ │ └── listsingle.h │ ├── spotfinder.m │ ├── spotfinder_default_detector.m │ ├── spotfinder_default_estimator.m │ ├── spotfinder_default_filter.m │ ├── spotfinder_default_threshold.m │ ├── spotfinder_getnames.m │ ├── subpix2d_fitquadric.m │ ├── subpix2d_gradintersect.m │ ├── threshold_boxmustd.m │ ├── threshold_fnc.m │ ├── threshold_mustd_val.m │ ├── threshold_std_val.m │ └── threshold_val.m │ └── yaml │ ├── README │ ├── YAML.m │ └── java │ ├── LICENSE-2.0.txt │ └── snakeyaml-1.9.jar ├── SIMToolbox1.20_MATLAB ├── ReadMe.txt ├── SIMToolbox.m ├── SIMToolbox.prj ├── config.m ├── license │ └── COPYING.txt ├── process.m ├── setEstimatePatterns.m ├── setFindPeaks.m ├── spotfinder_method_calibration.m ├── spotfinder_method_spotfinder.m └── utils │ ├── apodize │ ├── apodize_butterworth.m │ ├── apodize_circular.m │ ├── apodize_cosbell.m │ ├── apodize_gauss.m │ ├── apodize_lukosz.m │ ├── apodize_none.m │ ├── apodize_standard.m │ ├── apodize_triangle.m │ └── getapodizationnames.m │ ├── calibration │ ├── cal2Destim.cpp │ ├── cal2Destim.mexw32 │ ├── calconfig.m │ ├── calhomolin.m │ ├── calhomorad.m │ ├── cali2w.m │ ├── calload.m │ ├── calloadgdf.m │ ├── calprocess.m │ ├── calsave.m │ ├── calw2i.m │ ├── cart2sq.m │ ├── corners_detect.m │ ├── markers_check.m │ ├── markers_detect.m │ ├── markers_sort.m │ └── ptdist.m │ ├── image │ ├── fspecialseparable.m │ ├── imfilterseparable.m │ ├── imgadjust.m │ ├── imgclipval.m │ ├── imgflatfield.m │ ├── imgradprof.m │ └── imgrmpadding.m │ ├── io │ ├── cfgload.m │ ├── cfgsave.m │ ├── dimload.m │ ├── extractPathAndFilename.m │ ├── fileparts_dir.m │ ├── fileparts_name.m │ ├── fileparts_nameext.m │ ├── fixresname.m │ ├── imgdirinfo.m │ ├── imginfoinit.m │ ├── imgload.m │ ├── imgsave16.m │ ├── imgsave32.m │ ├── imgzload.m │ ├── iq2getinfo.m │ ├── iq2parse.m │ ├── isfile.m │ ├── loadtif.m │ └── tiffnumpg.m │ ├── misc │ ├── fftInterpolate.m │ ├── lmfit1DgaussXSAO.cpp │ ├── lmfit1DgaussXSAO.mexw32 │ ├── lmfit1DgaussXSAO.mexw64 │ ├── lmfit2DgaussXYSAO.cpp │ ├── lmfit2DgaussXYSAO.mexw32 │ ├── lmfit2DgaussXYSAO.mexw64 │ ├── lmmin │ │ ├── lm_eval.c │ │ ├── lmmin.c │ │ └── lmmin.h │ ├── locmax1d.m │ ├── m2c.m │ ├── printerror.m │ ├── rmfields.m │ ├── sigmoid.m │ ├── sizeof.m │ ├── structcat.m │ ├── timestamp.m │ └── whichcamera.m │ ├── patterns │ ├── ptrn2camera.m │ ├── ptrnchecklines.m │ ├── ptrnclose.m │ ├── ptrndirinfo.m │ ├── ptrngetimagenames.m │ ├── ptrngetnumro.m │ ├── ptrngetnumseq.m │ ├── ptrngetro.m │ ├── ptrnload.m │ ├── ptrnmaskprecompute.m │ └── ptrnopen.m │ ├── prepareData │ ├── gen_descfile.m │ ├── gen_ptrnest.m │ ├── gen_repfile.m │ ├── gen_repz.m │ ├── get_ptrnimagenames.m │ └── ro_lines.m │ ├── sim-msm │ ├── genMasks.m │ └── mapsim.m │ ├── sim-sr │ ├── sim_addOTF.m │ ├── sim_combine.m │ ├── sim_extract.m │ ├── sim_findpeaks.m │ ├── sim_findpeaksassign.m │ ├── sim_findpeaksloadimage.m │ ├── sim_matchspectra.m │ └── sim_shiftspectra.m │ ├── sim-vsm │ ├── getvsmnames.m │ ├── seqcfhomodyne.m │ ├── seqcfmaskonly.m │ ├── seqcfmaxmin.m │ ├── seqcfmaxmin2av.m │ ├── seqcfscaledsub.m │ ├── seqcfscaledsub1px.m │ ├── seqcfscaledsubbeta.m │ ├── seqopav.m │ ├── seqopmax.m │ ├── seqopmin.m │ ├── seqopsum.m │ ├── seqopsummaskoff.m │ ├── seqopsummaskon.m │ ├── seqsubseq.m │ └── seqwf.m │ ├── sim │ ├── runseqflatfield.m │ ├── seq2subseq.m │ ├── seqblure.m │ ├── seqfft2.m │ ├── seqflatfield.m │ ├── seqifft2.m │ ├── seqload.m │ ├── seqpadsmooth.m │ ├── seqremovemean.m │ ├── seqrewind.m │ └── seqstriperemoval.m │ ├── spotfinder │ ├── detector_locmax.m │ ├── estimator_lsq_fitquadric.m │ ├── estimator_lsq_gradintersect.m │ ├── estimator_none.m │ ├── filter_dao.m │ ├── filter_daoint.m │ ├── filter_diffav.m │ ├── filter_dog.m │ ├── filter_dogint.m │ ├── filter_gauss.m │ ├── filter_gaussint.m │ ├── filter_none.m │ ├── filter_wavelet.m │ ├── mex │ │ ├── boxmustd.cpp │ │ ├── boxmustd.mexw32 │ │ ├── boxmustd.mexw64 │ │ ├── circfilter.cpp │ │ ├── circfilter.mexw32 │ │ ├── circfilter.mexw64 │ │ ├── findlocmax2d.cpp │ │ ├── findlocmax2d.m │ │ ├── findlocmax2d.mexw32 │ │ ├── findlocmax2d.mexw64 │ │ └── listsingle.h │ ├── spotfinder.m │ ├── spotfinder_default_detector.m │ ├── spotfinder_default_estimator.m │ ├── spotfinder_default_filter.m │ ├── spotfinder_default_threshold.m │ ├── spotfinder_getnames.m │ ├── subpix2d_fitquadric.m │ ├── subpix2d_gradintersect.m │ ├── threshold_boxmustd.m │ ├── threshold_fnc.m │ ├── threshold_mustd_val.m │ ├── threshold_std_val.m │ └── threshold_val.m │ └── yaml │ ├── README │ ├── YAML.m │ └── java │ ├── LICENSE-2.0.txt │ └── snakeyaml-1.9.jar ├── SIMToolbox1.30_MATLAB ├── ReadMe.txt ├── SIMToolbox.m ├── _UPDATE_DOCUMENTATION_1.3.txt ├── config.m ├── license │ └── COPYING.txt ├── process.m ├── setEstimatePatterns.m ├── setFindPeaks.m ├── spotfinder_method_calibration.m ├── spotfinder_method_spotfinder.m └── utils │ ├── apodize │ ├── apodize_butterworth.m │ ├── apodize_circular.m │ ├── apodize_cosbell.m │ ├── apodize_gauss.m │ ├── apodize_lukosz.m │ ├── apodize_none.m │ ├── apodize_standard.m │ ├── apodize_triangle.m │ └── getapodizationnames.m │ ├── calibration │ ├── cal2Destim.cpp │ ├── cal2Destim.mexw32 │ ├── calconfig.m │ ├── calhomolin.m │ ├── calhomorad.m │ ├── cali2w.m │ ├── calload.m │ ├── calloadgdf.m │ ├── calprocess.m │ ├── calsave.m │ ├── calw2i.m │ ├── cart2sq.m │ ├── corners_detect.m │ ├── markers_check.m │ ├── markers_detect.m │ ├── markers_sort.m │ └── ptdist.m │ ├── image │ ├── fspecialseparable.m │ ├── imfilterseparable.m │ ├── imgadjust.m │ ├── imgclipval.m │ ├── imgflatfield.m │ ├── imgradprof.m │ └── imgrmpadding.m │ ├── io │ ├── cfgload.m │ ├── cfgsave.m │ ├── dimload.m │ ├── extractPathAndFilename.m │ ├── fileparts_dir.m │ ├── fileparts_name.m │ ├── fileparts_nameext.m │ ├── fixresname.m │ ├── imgdirinfo.m │ ├── imginfoinit.m │ ├── imgload.m │ ├── imgsave16.m │ ├── imgsave32.m │ ├── imgzload.m │ ├── iq2getinfo.m │ ├── iq2parse.m │ ├── isfile.m │ ├── loadtif.m │ └── tiffnumpg.m │ ├── misc │ ├── fftInterpolate.m │ ├── lmfit1DgaussXSAO.cpp │ ├── lmfit1DgaussXSAO.mexw32 │ ├── lmfit1DgaussXSAO.mexw64 │ ├── lmfit2DgaussXYSAO.cpp │ ├── lmfit2DgaussXYSAO.mexw32 │ ├── lmfit2DgaussXYSAO.mexw64 │ ├── lmmin │ │ ├── lm_eval.c │ │ ├── lmmin.c │ │ └── lmmin.h │ ├── locmax1d.m │ ├── m2c.m │ ├── printerror.m │ ├── rmfields.m │ ├── sigmoid.m │ ├── sizeof.m │ ├── structcat.m │ ├── timestamp.m │ └── whichcamera.m │ ├── patterns │ ├── ptrn2camera.m │ ├── ptrnchecklines.m │ ├── ptrnclose.m │ ├── ptrndirinfo.m │ ├── ptrngetimagenames.m │ ├── ptrngetnumro.m │ ├── ptrngetnumseq.m │ ├── ptrngetro.m │ ├── ptrnload.m │ ├── ptrnmaskprecompute.m │ └── ptrnopen.m │ ├── prepareData │ ├── deg2rad.m │ ├── gen_descfile.m │ ├── gen_ptrnest.m │ ├── gen_repfile.m │ ├── gen_repz.m │ ├── get_ptrnimagenames.m │ └── ro_lines.m │ ├── sim-msm │ ├── genMasks.m │ └── mapsim.m │ ├── sim-sr │ ├── sim_addOTF.m │ ├── sim_combine.m │ ├── sim_extract.m │ ├── sim_findpeaks.m │ ├── sim_findpeaksassign.m │ ├── sim_findpeaksloadimage.m │ ├── sim_matchspectra.m │ └── sim_shiftspectra.m │ ├── sim-vsm │ ├── getvsmnames.m │ ├── seqcfhomodyne.m │ ├── seqcfmaskonly.m │ ├── seqcfmaxmin.m │ ├── seqcfmaxmin2av.m │ ├── seqcfscaledsub.m │ ├── seqcfscaledsub1px.m │ ├── seqcfscaledsubbeta.m │ ├── seqopav.m │ ├── seqopmax.m │ ├── seqopmin.m │ ├── seqopsum.m │ ├── seqopsummaskoff.m │ ├── seqopsummaskon.m │ ├── seqsubseq.m │ └── seqwf.m │ ├── sim │ ├── runseqflatfield.m │ ├── seq2subseq.m │ ├── seqblure.m │ ├── seqfft2.m │ ├── seqflatfield.m │ ├── seqifft2.m │ ├── seqload.m │ ├── seqpadsmooth.m │ ├── seqremovemean.m │ ├── seqrewind.m │ └── seqstriperemoval.m │ ├── spotfinder │ ├── detector_locmax.m │ ├── estimator_lsq_fitquadric.m │ ├── estimator_lsq_gradintersect.m │ ├── estimator_none.m │ ├── filter_dao.m │ ├── filter_daoint.m │ ├── filter_diffav.m │ ├── filter_dog.m │ ├── filter_dogint.m │ ├── filter_gauss.m │ ├── filter_gaussint.m │ ├── filter_none.m │ ├── filter_wavelet.m │ ├── mex │ │ ├── boxmustd.cpp │ │ ├── boxmustd.mexw32 │ │ ├── boxmustd.mexw64 │ │ ├── circfilter.cpp │ │ ├── circfilter.mexw32 │ │ ├── circfilter.mexw64 │ │ ├── findlocmax2d.cpp │ │ ├── findlocmax2d.mexw32 │ │ ├── findlocmax2d.mexw64 │ │ └── listsingle.h │ ├── spotfinder.m │ ├── spotfinder_default_detector.m │ ├── spotfinder_default_estimator.m │ ├── spotfinder_default_filter.m │ ├── spotfinder_default_threshold.m │ ├── spotfinder_getnames.m │ ├── subpix2d_fitquadric.m │ ├── subpix2d_gradintersect.m │ ├── threshold_boxmustd.m │ ├── threshold_fnc.m │ ├── threshold_mustd_val.m │ ├── threshold_std_val.m │ └── threshold_val.m │ └── yaml │ ├── README │ ├── YAML.m │ └── java │ ├── LICENSE-2.0.txt │ └── snakeyaml-1.9.jar ├── SIMToolbox1.31_MATLAB ├── ReadMe.txt ├── SIMToolbox.m ├── config.m ├── license │ └── COPYING.txt ├── process.m ├── setEstimatePatterns.m ├── setFindPeaks.m ├── spotfinder_method_calibration.m ├── spotfinder_method_spotfinder.m └── utils │ ├── apodize │ ├── apodize_butterworth.m │ ├── apodize_circular.m │ ├── apodize_cosbell.m │ ├── apodize_gauss.m │ ├── apodize_lukosz.m │ ├── apodize_none.m │ ├── apodize_standard.m │ ├── apodize_triangle.m │ └── getapodizationnames.m │ ├── calibration │ ├── cal2Destim.cpp │ ├── cal2Destim.mexw32 │ ├── calconfig.m │ ├── calhomolin.m │ ├── calhomorad.m │ ├── cali2w.m │ ├── calload.m │ ├── calloadgdf.m │ ├── calprocess.m │ ├── calsave.m │ ├── calw2i.m │ ├── cart2sq.m │ ├── corners_detect.m │ ├── markers_check.m │ ├── markers_detect.m │ ├── markers_sort.m │ └── ptdist.m │ ├── image │ ├── fspecialseparable.m │ ├── imfilterseparable.m │ ├── imgadjust.m │ ├── imgclipval.m │ ├── imgflatfield.m │ ├── imgradprof.m │ └── imgrmpadding.m │ ├── io │ ├── cfgload.m │ ├── cfgsave.m │ ├── dimload.m │ ├── extractPathAndFilename.m │ ├── fileparts_dir.m │ ├── fileparts_name.m │ ├── fileparts_nameext.m │ ├── fixresname.m │ ├── imgdirinfo.m │ ├── imginfoinit.m │ ├── imgload.m │ ├── imgsave16.m │ ├── imgsave32.m │ ├── imgzload.m │ ├── iq2getinfo.m │ ├── iq2parse.m │ ├── isfile.m │ ├── loadtif.m │ └── tiffnumpg.m │ ├── misc │ ├── fftInterpolate.m │ ├── lmfit1DgaussXSAO.cpp │ ├── lmfit1DgaussXSAO.mexw32 │ ├── lmfit1DgaussXSAO.mexw64 │ ├── lmfit2DgaussXYSAO.cpp │ ├── lmfit2DgaussXYSAO.mexw32 │ ├── lmfit2DgaussXYSAO.mexw64 │ ├── lmmin │ │ ├── lm_eval.c │ │ ├── lmmin.c │ │ └── lmmin.h │ ├── locmax1d.m │ ├── m2c.m │ ├── printerror.m │ ├── rmfields.m │ ├── sigmoid.m │ ├── sizeof.m │ ├── structcat.m │ ├── timestamp.m │ └── whichcamera.m │ ├── patterns │ ├── ptrn2camera.m │ ├── ptrnchecklines.m │ ├── ptrnclose.m │ ├── ptrndirinfo.m │ ├── ptrngetimagenames.m │ ├── ptrngetnumro.m │ ├── ptrngetnumseq.m │ ├── ptrngetro.m │ ├── ptrnload.m │ ├── ptrnmaskprecompute.m │ └── ptrnopen.m │ ├── prepareData │ ├── deg2rad.m │ ├── gen_descfile.m │ ├── gen_ptrnest.m │ ├── gen_repfile.m │ ├── gen_repz.m │ ├── get_ptrnimagenames.m │ └── ro_lines.m │ ├── sim-msm │ ├── genMasks.m │ └── mapsim.m │ ├── sim-sr │ ├── sim_addOTF.m │ ├── sim_combine.m │ ├── sim_extract.m │ ├── sim_findpeaks.m │ ├── sim_findpeaksassign.m │ ├── sim_findpeaksloadimage.m │ ├── sim_matchspectra.m │ └── sim_shiftspectra.m │ ├── sim-vsm │ ├── getvsmnames.m │ ├── seqcfhomodyne.m │ ├── seqcfmaskonly.m │ ├── seqcfmaxmin.m │ ├── seqcfmaxmin2av.m │ ├── seqcfscaledsub.m │ ├── seqcfscaledsub1px.m │ ├── seqcfscaledsubbeta.m │ ├── seqopav.m │ ├── seqopmax.m │ ├── seqopmin.m │ ├── seqopsum.m │ ├── seqopsummaskoff.m │ ├── seqopsummaskon.m │ ├── seqsubseq.m │ └── seqwf.m │ ├── sim │ ├── runseqflatfield.m │ ├── seq2subseq.m │ ├── seqblure.m │ ├── seqfft2.m │ ├── seqflatfield.m │ ├── seqifft2.m │ ├── seqload.m │ ├── seqpadsmooth.m │ ├── seqremovemean.m │ ├── seqrewind.m │ └── seqstriperemoval.m │ ├── spotfinder │ ├── detector_locmax.m │ ├── estimator_lsq_fitquadric.m │ ├── estimator_lsq_gradintersect.m │ ├── estimator_none.m │ ├── filter_dao.m │ ├── filter_daoint.m │ ├── filter_diffav.m │ ├── filter_dog.m │ ├── filter_dogint.m │ ├── filter_gauss.m │ ├── filter_gaussint.m │ ├── filter_none.m │ ├── filter_wavelet.m │ ├── mex │ │ ├── boxmustd.cpp │ │ ├── boxmustd.mexw32 │ │ ├── boxmustd.mexw64 │ │ ├── circfilter.cpp │ │ ├── circfilter.mexw32 │ │ ├── circfilter.mexw64 │ │ ├── findlocmax2d.cpp │ │ ├── findlocmax2d.mexw32 │ │ ├── findlocmax2d.mexw64 │ │ └── listsingle.h │ ├── spotfinder.m │ ├── spotfinder_default_detector.m │ ├── spotfinder_default_estimator.m │ ├── spotfinder_default_filter.m │ ├── spotfinder_default_threshold.m │ ├── spotfinder_getnames.m │ ├── subpix2d_fitquadric.m │ ├── subpix2d_gradintersect.m │ ├── threshold_boxmustd.m │ ├── threshold_fnc.m │ ├── threshold_mustd_val.m │ ├── threshold_std_val.m │ └── threshold_val.m │ └── yaml │ ├── README │ ├── YAML.m │ └── java │ ├── LICENSE-2.0.txt │ └── snakeyaml-1.9.jar ├── SIMToolbox1.32_MATLAB ├── ReadMe.txt ├── SIMToolbox.m ├── config.m ├── license │ └── COPYING.txt ├── process.m ├── setEstimatePatterns.m ├── setFindPeaks.m ├── spotfinder_method_calibration.m ├── spotfinder_method_spotfinder.m └── utils │ ├── apodize │ ├── apodize_butterworth.m │ ├── apodize_circular.m │ ├── apodize_cosbell.m │ ├── apodize_gauss.m │ ├── apodize_lukosz.m │ ├── apodize_none.m │ ├── apodize_standard.m │ ├── apodize_triangle.m │ └── getapodizationnames.m │ ├── calibration │ ├── cal2Destim.cpp │ ├── cal2Destim.mexw32 │ ├── calconfig.m │ ├── calhomolin.m │ ├── calhomorad.m │ ├── cali2w.m │ ├── calload.m │ ├── calloadgdf.m │ ├── calprocess.m │ ├── calsave.m │ ├── calw2i.m │ ├── cart2sq.m │ ├── corners_detect.m │ ├── markers_check.m │ ├── markers_detect.m │ ├── markers_sort.m │ └── ptdist.m │ ├── image │ ├── fspecialseparable.m │ ├── imfilterseparable.m │ ├── imgadjust.m │ ├── imgclipval.m │ ├── imgflatfield.m │ ├── imgradprof.m │ └── imgrmpadding.m │ ├── io │ ├── cfgload.m │ ├── cfgsave.m │ ├── dimload.m │ ├── extractPathAndFilename.m │ ├── fileparts_dir.m │ ├── fileparts_name.m │ ├── fileparts_nameext.m │ ├── fixresname.m │ ├── imgdirinfo.m │ ├── imginfoinit.m │ ├── imgload.m │ ├── imgsave16.m │ ├── imgsave32.m │ ├── imgzload.m │ ├── iq2getinfo.m │ ├── iq2parse.m │ ├── isfile.m │ ├── loadtif.m │ └── tiffnumpg.m │ ├── misc │ ├── fftInterpolate.m │ ├── lmfit1DgaussXSAO.cpp │ ├── lmfit1DgaussXSAO.mexw32 │ ├── lmfit1DgaussXSAO.mexw64 │ ├── lmfit2DgaussXYSAO.cpp │ ├── lmfit2DgaussXYSAO.mexw32 │ ├── lmfit2DgaussXYSAO.mexw64 │ ├── lmmin │ │ ├── lm_eval.c │ │ ├── lmmin.c │ │ └── lmmin.h │ ├── locmax1d.m │ ├── m2c.m │ ├── printerror.m │ ├── rmfields.m │ ├── sigmoid.m │ ├── sizeof.m │ ├── structcat.m │ ├── timestamp.m │ └── whichcamera.m │ ├── patterns │ ├── ptrn2camera.m │ ├── ptrnchecklines.m │ ├── ptrnclose.m │ ├── ptrndirinfo.m │ ├── ptrngetimagenames.m │ ├── ptrngetnumro.m │ ├── ptrngetnumseq.m │ ├── ptrngetro.m │ ├── ptrnload.m │ ├── ptrnmaskprecompute.m │ └── ptrnopen.m │ ├── prepareData │ ├── deg2rad.m │ ├── gen_descfile.m │ ├── gen_ptrnest.m │ ├── gen_repfile.m │ ├── gen_repz.m │ ├── get_ptrnimagenames.m │ └── ro_lines.m │ ├── sim-msm │ ├── genMasks.m │ └── mapsim.m │ ├── sim-sr │ ├── sim_addOTF.m │ ├── sim_combine.m │ ├── sim_extract.m │ ├── sim_findpeaks.m │ ├── sim_findpeaksassign.m │ ├── sim_findpeaksloadimage.m │ ├── sim_matchspectra.m │ └── sim_shiftspectra.m │ ├── sim-vsm │ ├── getvsmnames.m │ ├── seqcfhomodyne.m │ ├── seqcfmaskonly.m │ ├── seqcfmaxmin.m │ ├── seqcfmaxmin2av.m │ ├── seqcfscaledsub.m │ ├── seqcfscaledsub1px.m │ ├── seqcfscaledsubbeta.m │ ├── seqopav.m │ ├── seqopmax.m │ ├── seqopmin.m │ ├── seqopsum.m │ ├── seqopsummaskoff.m │ ├── seqopsummaskon.m │ ├── seqsubseq.m │ └── seqwf.m │ ├── sim │ ├── runseqflatfield.m │ ├── seq2subseq.m │ ├── seqblure.m │ ├── seqfft2.m │ ├── seqflatfield.m │ ├── seqifft2.m │ ├── seqload.m │ ├── seqpadsmooth.m │ ├── seqremovemean.m │ ├── seqrewind.m │ └── seqstriperemoval.m │ ├── spotfinder │ ├── detector_locmax.m │ ├── estimator_lsq_fitquadric.m │ ├── estimator_lsq_gradintersect.m │ ├── estimator_none.m │ ├── filter_dao.m │ ├── filter_daoint.m │ ├── filter_diffav.m │ ├── filter_dog.m │ ├── filter_dogint.m │ ├── filter_gauss.m │ ├── filter_gaussint.m │ ├── filter_none.m │ ├── filter_wavelet.m │ ├── mex │ │ ├── boxmustd.cpp │ │ ├── boxmustd.mexw32 │ │ ├── boxmustd.mexw64 │ │ ├── circfilter.cpp │ │ ├── circfilter.mexw32 │ │ ├── circfilter.mexw64 │ │ ├── findlocmax2d.cpp │ │ ├── findlocmax2d.mexw32 │ │ ├── findlocmax2d.mexw64 │ │ └── listsingle.h │ ├── spotfinder.m │ ├── spotfinder_default_detector.m │ ├── spotfinder_default_estimator.m │ ├── spotfinder_default_filter.m │ ├── spotfinder_default_threshold.m │ ├── spotfinder_getnames.m │ ├── subpix2d_fitquadric.m │ ├── subpix2d_gradintersect.m │ ├── threshold_boxmustd.m │ ├── threshold_fnc.m │ ├── threshold_mustd_val.m │ ├── threshold_std_val.m │ └── threshold_val.m │ └── yaml │ ├── README │ ├── YAML.m │ └── java │ ├── LICENSE-2.0.txt │ └── snakeyaml-1.9.jar ├── SIMToolbox1.33_MATLAB ├── ReadMe.txt ├── SIMToolbox.m ├── UPDATE_DOCUMENTATION_v1.33.txt ├── config.m ├── license │ └── COPYING.txt ├── process.m ├── setEstimatePatterns.m ├── setFindPeaks.m ├── spotfinder_method_calibration.m ├── spotfinder_method_spotfinder.m └── utils │ ├── apodize │ ├── apodize_butterworth.m │ ├── apodize_circular.m │ ├── apodize_cosbell.m │ ├── apodize_gauss.m │ ├── apodize_lukosz.m │ ├── apodize_none.m │ ├── apodize_standard.m │ ├── apodize_triangle.m │ └── getapodizationnames.m │ ├── calibration │ ├── cal2Destim.cpp │ ├── cal2Destim.mexw32 │ ├── calconfig.m │ ├── calhomolin.m │ ├── calhomorad.m │ ├── cali2w.m │ ├── calload.m │ ├── calloadgdf.m │ ├── calprocess.m │ ├── calsave.m │ ├── calw2i.m │ ├── cart2sq.m │ ├── corners_detect.m │ ├── markers_check.m │ ├── markers_detect.m │ ├── markers_sort.m │ └── ptdist.m │ ├── image │ ├── fspecialseparable.m │ ├── imfilterseparable.m │ ├── imgadjust.m │ ├── imgclipval.m │ ├── imgflatfield.m │ ├── imgradprof.m │ └── imgrmpadding.m │ ├── io │ ├── cfgload.m │ ├── cfgsave.m │ ├── dimload.m │ ├── extractPathAndFilename.m │ ├── fileparts_dir.m │ ├── fileparts_name.m │ ├── fileparts_nameext.m │ ├── fixresname.m │ ├── imgdirinfo.m │ ├── imginfoinit.m │ ├── imgload.m │ ├── imgsave16.m │ ├── imgsave32.m │ ├── imgzload.m │ ├── iq2getinfo.m │ ├── iq2parse.m │ ├── isfile.m │ ├── loadtif.m │ └── tiffnumpg.m │ ├── misc │ ├── fftInterpolate.m │ ├── lmfit1DgaussXSAO.cpp │ ├── lmfit1DgaussXSAO.mexw32 │ ├── lmfit1DgaussXSAO.mexw64 │ ├── lmfit2DgaussXYSAO.cpp │ ├── lmfit2DgaussXYSAO.mexw32 │ ├── lmfit2DgaussXYSAO.mexw64 │ ├── lmmin │ │ ├── lm_eval.c │ │ ├── lmmin.c │ │ └── lmmin.h │ ├── locmax1d.m │ ├── m2c.m │ ├── printerror.m │ ├── rmfields.m │ ├── sigmoid.m │ ├── sizeof.m │ ├── structcat.m │ ├── timestamp.m │ └── whichcamera.m │ ├── patterns │ ├── ptrn2camera.m │ ├── ptrnchecklines.m │ ├── ptrnclose.m │ ├── ptrndirinfo.m │ ├── ptrngetimagenames.m │ ├── ptrngetnumro.m │ ├── ptrngetnumseq.m │ ├── ptrngetro.m │ ├── ptrnload.m │ ├── ptrnmaskprecompute.m │ └── ptrnopen.m │ ├── prepareData │ ├── deg2rad.m │ ├── gen_descfile.m │ ├── gen_ptrnest.m │ ├── gen_repfile.m │ ├── gen_repz.m │ ├── get_ptrnimagenames.m │ └── ro_lines.m │ ├── sim-msm │ ├── genMasks.m │ └── mapsim.m │ ├── sim-sr │ ├── sim_addOTF.m │ ├── sim_combine.m │ ├── sim_extract.m │ ├── sim_findpeaks.m │ ├── sim_findpeaksassign.m │ ├── sim_findpeaksloadimage.m │ ├── sim_matchspectra.m │ └── sim_shiftspectra.m │ ├── sim-vsm │ ├── getvsmnames.m │ ├── seqcfhomodyne.m │ ├── seqcfmaskonly.m │ ├── seqcfmaxmin.m │ ├── seqcfmaxmin2av.m │ ├── seqcfscaledsub.m │ ├── seqcfscaledsub1px.m │ ├── seqcfscaledsubbeta.m │ ├── seqopav.m │ ├── seqopmax.m │ ├── seqopmin.m │ ├── seqopsum.m │ ├── seqopsummaskoff.m │ ├── seqopsummaskon.m │ ├── seqsubseq.m │ └── seqwf.m │ ├── sim │ ├── runseqflatfield.m │ ├── seq2subseq.m │ ├── seqblure.m │ ├── seqfft2.m │ ├── seqflatfield.m │ ├── seqifft2.m │ ├── seqload.m │ ├── seqpadsmooth.m │ ├── seqremovemean.m │ ├── seqrewind.m │ └── seqstriperemoval.m │ ├── spotfinder │ ├── detector_locmax.m │ ├── estimator_lsq_fitquadric.m │ ├── estimator_lsq_gradintersect.m │ ├── estimator_none.m │ ├── filter_dao.m │ ├── filter_daoint.m │ ├── filter_diffav.m │ ├── filter_dog.m │ ├── filter_dogint.m │ ├── filter_gauss.m │ ├── filter_gaussint.m │ ├── filter_none.m │ ├── filter_wavelet.m │ ├── mex │ │ ├── boxmustd.cpp │ │ ├── boxmustd.mexw32 │ │ ├── boxmustd.mexw64 │ │ ├── circfilter.cpp │ │ ├── circfilter.mexw32 │ │ ├── circfilter.mexw64 │ │ ├── findlocmax2d.cpp │ │ ├── findlocmax2d.mexw32 │ │ ├── findlocmax2d.mexw64 │ │ └── listsingle.h │ ├── spotfinder.m │ ├── spotfinder_default_detector.m │ ├── spotfinder_default_estimator.m │ ├── spotfinder_default_filter.m │ ├── spotfinder_default_threshold.m │ ├── spotfinder_getnames.m │ ├── subpix2d_fitquadric.m │ ├── subpix2d_gradintersect.m │ ├── threshold_boxmustd.m │ ├── threshold_fnc.m │ ├── threshold_mustd_val.m │ ├── threshold_std_val.m │ └── threshold_val.m │ └── yaml │ ├── README │ ├── YAML.m │ └── java │ ├── LICENSE-2.0.txt │ └── snakeyaml-1.9.jar ├── SIMToolbox1.34_MATLAB ├── ReadMe.txt ├── SIMToolbox.m ├── UPDATE_DOCUMENTATION_v1.34.txt ├── config.m ├── license │ └── COPYING.txt ├── process.m ├── setEstimatePatterns.m ├── setFindPeaks.m ├── spotfinder_method_calibration.m ├── spotfinder_method_spotfinder.m └── utils │ ├── apodize │ ├── apodize_butterworth.m │ ├── apodize_circular.m │ ├── apodize_cosbell.m │ ├── apodize_gauss.m │ ├── apodize_lukosz.m │ ├── apodize_none.m │ ├── apodize_standard.m │ ├── apodize_triangle.m │ └── getapodizationnames.m │ ├── calibration │ ├── cal2Destim.cpp │ ├── cal2Destim.mexw32 │ ├── calconfig.m │ ├── calhomolin.m │ ├── calhomorad.m │ ├── cali2w.m │ ├── calload.m │ ├── calloadgdf.m │ ├── calprocess.m │ ├── calsave.m │ ├── calw2i.m │ ├── cart2sq.m │ ├── corners_detect.m │ ├── markers_check.m │ ├── markers_detect.m │ ├── markers_sort.m │ └── ptdist.m │ ├── image │ ├── fspecialseparable.m │ ├── imfilterseparable.m │ ├── imgadjust.m │ ├── imgclipval.m │ ├── imgflatfield.m │ ├── imgradprof.m │ └── imgrmpadding.m │ ├── io │ ├── cfgload.m │ ├── cfgsave.m │ ├── dimload.m │ ├── extractPathAndFilename.m │ ├── fileparts_dir.m │ ├── fileparts_name.m │ ├── fileparts_nameext.m │ ├── fixresname.m │ ├── imgdirinfo.m │ ├── imginfoinit.m │ ├── imgload.m │ ├── imgsave16.m │ ├── imgsave32.m │ ├── imgzload.m │ ├── iq2getinfo.m │ ├── iq2parse.m │ ├── isfile.m │ ├── loadtif.m │ └── tiffnumpg.m │ ├── misc │ ├── fftInterpolate.m │ ├── lmfit1DgaussXSAO.cpp │ ├── lmfit1DgaussXSAO.mexw32 │ ├── lmfit1DgaussXSAO.mexw64 │ ├── lmfit2DgaussXYSAO.cpp │ ├── lmfit2DgaussXYSAO.mexw32 │ ├── lmfit2DgaussXYSAO.mexw64 │ ├── lmmin │ │ ├── lm_eval.c │ │ ├── lmmin.c │ │ └── lmmin.h │ ├── locmax1d.m │ ├── m2c.m │ ├── printerror.m │ ├── rmfields.m │ ├── sigmoid.m │ ├── sizeof.m │ ├── structcat.m │ ├── timestamp.m │ └── whichcamera.m │ ├── patterns │ ├── ptrn2camera.m │ ├── ptrnchecklines.m │ ├── ptrnclose.m │ ├── ptrndirinfo.m │ ├── ptrngetimagenames.m │ ├── ptrngetnumro.m │ ├── ptrngetnumseq.m │ ├── ptrngetro.m │ ├── ptrnload.m │ ├── ptrnmaskprecompute.m │ └── ptrnopen.m │ ├── prepareData │ ├── deg2rad.m │ ├── gen_descfile.m │ ├── gen_ptrnest.m │ ├── gen_repfile.m │ ├── gen_repz.m │ ├── get_ptrnimagenames.m │ └── ro_lines.m │ ├── sim-msm │ ├── genMasks.m │ └── mapsim.m │ ├── sim-sr │ ├── sim_addOTF.m │ ├── sim_combine.m │ ├── sim_extract.m │ ├── sim_findpeaks.m │ ├── sim_findpeaksassign.m │ ├── sim_findpeaksloadimage.m │ ├── sim_matchspectra.m │ └── sim_shiftspectra.m │ ├── sim-vsm │ ├── getvsmnames.m │ ├── seqcfhomodyne.m │ ├── seqcfmaskonly.m │ ├── seqcfmaxmin.m │ ├── seqcfmaxmin2av.m │ ├── seqcfscaledsub.m │ ├── seqcfscaledsub1px.m │ ├── seqcfscaledsubbeta.m │ ├── seqopav.m │ ├── seqopmax.m │ ├── seqopmin.m │ ├── seqopsum.m │ ├── seqopsummaskoff.m │ ├── seqopsummaskon.m │ ├── seqsubseq.m │ └── seqwf.m │ ├── sim │ ├── runseqflatfield.m │ ├── seq2subseq.m │ ├── seqblure.m │ ├── seqfft2.m │ ├── seqflatfield.m │ ├── seqifft2.m │ ├── seqload.m │ ├── seqpadsmooth.m │ ├── seqremovemean.m │ ├── seqrewind.m │ └── seqstriperemoval.m │ ├── spotfinder │ ├── detector_locmax.m │ ├── estimator_lsq_fitquadric.m │ ├── estimator_lsq_gradintersect.m │ ├── estimator_none.m │ ├── filter_dao.m │ ├── filter_daoint.m │ ├── filter_diffav.m │ ├── filter_dog.m │ ├── filter_dogint.m │ ├── filter_gauss.m │ ├── filter_gaussint.m │ ├── filter_none.m │ ├── filter_wavelet.m │ ├── mex │ │ ├── boxmustd.cpp │ │ ├── boxmustd.mexw32 │ │ ├── boxmustd.mexw64 │ │ ├── circfilter.cpp │ │ ├── circfilter.mexw32 │ │ ├── circfilter.mexw64 │ │ ├── findlocmax2d.cpp │ │ ├── findlocmax2d.mexw32 │ │ ├── findlocmax2d.mexw64 │ │ └── listsingle.h │ ├── spotfinder.m │ ├── spotfinder_default_detector.m │ ├── spotfinder_default_estimator.m │ ├── spotfinder_default_filter.m │ ├── spotfinder_default_threshold.m │ ├── spotfinder_getnames.m │ ├── subpix2d_fitquadric.m │ ├── subpix2d_gradintersect.m │ ├── threshold_boxmustd.m │ ├── threshold_fnc.m │ ├── threshold_mustd_val.m │ ├── threshold_std_val.m │ └── threshold_val.m │ └── yaml │ ├── README │ ├── YAML.m │ └── java │ ├── LICENSE-2.0.txt │ └── snakeyaml-1.9.jar ├── SIMToolbox2.00_MATLAB ├── ReadMe.txt ├── SIMToolbox.m ├── _UPDATE_DOCUMENTATION_2.0.txt ├── config.m ├── license │ ├── COPYING.txt │ └── sim_logo.bmp ├── process.m ├── setEstimatePatterns.m ├── setFindPeaks.m ├── spotfinder_method_calibration.m ├── spotfinder_method_spotfinder.m └── utils │ ├── apodize │ ├── apodize_butterworth.m │ ├── apodize_circular.m │ ├── apodize_cosbell.m │ ├── apodize_gauss.m │ ├── apodize_lukosz.m │ ├── apodize_none.m │ ├── apodize_standard.m │ ├── apodize_triangle.m │ └── getapodizationnames.m │ ├── calibration │ ├── cal2Destim.cpp │ ├── cal2Destim.mexw32 │ ├── calconfig.m │ ├── calhomolin.m │ ├── calhomorad.m │ ├── cali2w.m │ ├── calload.m │ ├── calloadgdf.m │ ├── calprocess.m │ ├── calsave.m │ ├── calw2i.m │ ├── cart2sq.m │ ├── corners_detect.m │ ├── markers_check.m │ ├── markers_detect.m │ ├── markers_sort.m │ └── ptdist.m │ ├── image │ ├── fspecialseparable.m │ ├── imfilterseparable.m │ ├── imgadjust.m │ ├── imgclipval.m │ ├── imgflatfield.m │ ├── imgradprof.m │ └── imgrmpadding.m │ ├── io │ ├── cfgload.m │ ├── cfgsave.m │ ├── dimload.m │ ├── extractPathAndFilename.m │ ├── fileparts_dir.m │ ├── fileparts_name.m │ ├── fileparts_nameext.m │ ├── fixresname.m │ ├── imgdirinfo.m │ ├── imginfoinit.m │ ├── imgload.m │ ├── imgsave16.m │ ├── imgsave16_2.m │ ├── imgsave32.m │ ├── imgzload.m │ ├── iq2getinfo.m │ ├── iq2parse.m │ ├── isfile.m │ ├── loadtif.m │ └── tiffnumpg.m │ ├── misc │ ├── fftInterpolate.m │ ├── lmfit1DgaussXSAO.cpp │ ├── lmfit1DgaussXSAO.mexw32 │ ├── lmfit1DgaussXSAO.mexw64 │ ├── lmfit2DgaussXYSAO.cpp │ ├── lmfit2DgaussXYSAO.mexw32 │ ├── lmfit2DgaussXYSAO.mexw64 │ ├── lmmin │ │ ├── lm_eval.c │ │ ├── lmmin.c │ │ └── lmmin.h │ ├── locmax1d.m │ ├── m2c.m │ ├── printerror.m │ ├── rmfields.m │ ├── sigmoid.m │ ├── sizeof.m │ ├── structcat.m │ ├── timestamp.m │ └── whichcamera.m │ ├── patterns │ ├── ptrn2camera.m │ ├── ptrnchecklines.m │ ├── ptrnclose.m │ ├── ptrndirinfo.m │ ├── ptrngetimagenames.m │ ├── ptrngetnumro.m │ ├── ptrngetnumseq.m │ ├── ptrngetro.m │ ├── ptrnload.m │ ├── ptrnmaskprecompute.m │ └── ptrnopen.m │ ├── prepareData │ ├── deg2rad.m │ ├── gen_descfile.m │ ├── gen_ptrnest.m │ ├── gen_ptrnest_orig.m │ ├── gen_repfile.m │ ├── gen_repz.m │ ├── get_ptrnimagenames.m │ └── ro_lines.m │ ├── sim-msm │ ├── CPU │ │ └── mapcore.m │ ├── CUDA │ │ └── MapcoreCuda.mexw64 │ ├── apodize.m │ ├── applyOTF.m │ ├── createOTF.m │ ├── estimateNoise.m │ ├── genMasks.m │ ├── imnorm.m │ ├── mapsim.m │ └── spectralMask.m │ ├── sim-sr │ ├── sim_addOTF.m │ ├── sim_combine.m │ ├── sim_extract.m │ ├── sim_findpeaks.m │ ├── sim_findpeaks_corr.m │ ├── sim_findpeaksassign.m │ ├── sim_findpeaksloadimage.m │ ├── sim_matchspectra.m │ └── sim_shiftspectra.m │ ├── sim-vsm │ ├── getvsmnames.m │ ├── seqcfhomodyne.m │ ├── seqcfmaskonly.m │ ├── seqcfmaxmin.m │ ├── seqcfmaxmin2av.m │ ├── seqcfscaledsub.m │ ├── seqcfscaledsub1px.m │ ├── seqcfscaledsubbeta.m │ ├── seqopav.m │ ├── seqopmax.m │ ├── seqopmin.m │ ├── seqopsum.m │ ├── seqopsummaskoff.m │ ├── seqopsummaskon.m │ ├── seqsubseq.m │ └── seqwf.m │ ├── sim │ ├── runseqflatfield.m │ ├── seq2subseq.m │ ├── seqblure.m │ ├── seqfft2.m │ ├── seqflatfield.m │ ├── seqifft2.m │ ├── seqload.m │ ├── seqpadsmooth.m │ ├── seqremovemean.m │ ├── seqrewind.m │ └── seqstriperemoval.m │ ├── spotfinder │ ├── detector_locmax.m │ ├── estimator_lsq_fitquadric.m │ ├── estimator_lsq_gradintersect.m │ ├── estimator_none.m │ ├── filter_dao.m │ ├── filter_daoint.m │ ├── filter_diffav.m │ ├── filter_dog.m │ ├── filter_dogint.m │ ├── filter_gauss.m │ ├── filter_gaussint.m │ ├── filter_none.m │ ├── filter_wavelet.m │ ├── mex │ │ ├── boxmustd.cpp │ │ ├── boxmustd.mexw32 │ │ ├── boxmustd.mexw64 │ │ ├── circfilter.cpp │ │ ├── circfilter.mexw32 │ │ ├── circfilter.mexw64 │ │ ├── findlocmax2d.cpp │ │ ├── findlocmax2d.mexw32 │ │ ├── findlocmax2d.mexw64 │ │ └── listsingle.h │ ├── spotfinder.m │ ├── spotfinder_default_detector.m │ ├── spotfinder_default_estimator.m │ ├── spotfinder_default_filter.m │ ├── spotfinder_default_threshold.m │ ├── spotfinder_getnames.m │ ├── subpix2d_fitquadric.m │ ├── subpix2d_gradintersect.m │ ├── threshold_boxmustd.m │ ├── threshold_fnc.m │ ├── threshold_mustd_val.m │ ├── threshold_std_val.m │ └── threshold_val.m │ └── yaml │ ├── README │ ├── YAML.m │ └── java │ ├── LICENSE-2.0.txt │ └── snakeyaml-1.9.jar ├── SIMToolbox2.10_MATLAB ├── ReadMe.txt ├── SIMToolbox.m ├── _UPDATE_DOCUMENTATION_2.1.txt ├── config.m ├── license │ ├── COPYING.txt │ └── sim_logo.bmp ├── process.m ├── setEstimatePatterns.m ├── setFindPeaks.m ├── spotfinder_method_calibration.m ├── spotfinder_method_spotfinder.m └── utils │ ├── apodize │ ├── apodize_butterworth.m │ ├── apodize_circular.m │ ├── apodize_cosbell.m │ ├── apodize_gauss.m │ ├── apodize_lukosz.m │ ├── apodize_none.m │ ├── apodize_standard.m │ ├── apodize_triangle.m │ └── getapodizationnames.m │ ├── calibration │ ├── cal2Destim.cpp │ ├── cal2Destim.mexw32 │ ├── calconfig.m │ ├── calhomolin.m │ ├── calhomorad.m │ ├── cali2w.m │ ├── calload.m │ ├── calloadgdf.m │ ├── calprocess.m │ ├── calsave.m │ ├── calw2i.m │ ├── cart2sq.m │ ├── corners_detect.m │ ├── markers_check.m │ ├── markers_detect.m │ ├── markers_sort.m │ └── ptdist.m │ ├── image │ ├── fspecialseparable.m │ ├── imfilterseparable.m │ ├── imgadjust.m │ ├── imgclipval.m │ ├── imgflatfield.m │ ├── imgradprof.m │ └── imgrmpadding.m │ ├── io │ ├── cfgload.m │ ├── cfgsave.m │ ├── dimload.m │ ├── extractPathAndFilename.m │ ├── fileparts_dir.m │ ├── fileparts_name.m │ ├── fileparts_nameext.m │ ├── fixresname.m │ ├── imgdirinfo.m │ ├── imginfoinit.m │ ├── imgload.m │ ├── imgsave16.m │ ├── imgsave32.m │ ├── imgzload.m │ ├── iq2getinfo.m │ ├── iq2parse.m │ ├── isfile.m │ ├── loadtif.m │ └── tiffnumpg.m │ ├── misc │ ├── fftInterpolate.m │ ├── lmfit1DgaussXSAO.cpp │ ├── lmfit1DgaussXSAO.mexw32 │ ├── lmfit1DgaussXSAO.mexw64 │ ├── lmfit2DgaussXYSAO.cpp │ ├── lmfit2DgaussXYSAO.mexw32 │ ├── lmfit2DgaussXYSAO.mexw64 │ ├── lmmin │ │ ├── lm_eval.c │ │ ├── lmmin.c │ │ └── lmmin.h │ ├── locmax1d.m │ ├── m2c.m │ ├── printerror.m │ ├── rmfields.m │ ├── sigmoid.m │ ├── sizeof.m │ ├── structcat.m │ ├── timestamp.m │ └── whichcamera.m │ ├── patterns │ ├── ptrn2camera.m │ ├── ptrnchecklines.m │ ├── ptrnclose.m │ ├── ptrndirinfo.m │ ├── ptrngetimagenames.m │ ├── ptrngetnumro.m │ ├── ptrngetnumseq.m │ ├── ptrngetro.m │ ├── ptrnload.m │ ├── ptrnmaskprecompute.m │ └── ptrnopen.m │ ├── prepareData │ ├── deg2rad.m │ ├── gen_descfile.m │ ├── gen_ptrnest.m │ ├── gen_ptrnest_orig.m │ ├── gen_repfile.m │ ├── gen_repz.m │ ├── get_ptrnimagenames.m │ └── ro_lines.m │ ├── sim-msm │ ├── CPU │ │ └── mapcore.m │ ├── CUDA │ │ └── MapcoreCuda.mexw64 │ ├── apodize.m │ ├── applyOTF.m │ ├── createOTF.m │ ├── estimateNoise.m │ ├── genMasks.m │ ├── imnorm.m │ ├── mapsim.m │ └── spectralMask.m │ ├── sim-sr │ ├── sim_addOTF.m │ ├── sim_combine.m │ ├── sim_extract.m │ ├── sim_findpeaks.m │ ├── sim_findpeaks_corr.m │ ├── sim_findpeaksassign.m │ ├── sim_findpeaksloadimage.m │ ├── sim_matchspectra.m │ └── sim_shiftspectra.m │ ├── sim-vsm │ ├── getvsmnames.m │ ├── seqcfhomodyne.m │ ├── seqcfmaskonly.m │ ├── seqcfmaxmin.m │ ├── seqcfmaxmin2av.m │ ├── seqcfscaledsub.m │ ├── seqcfscaledsub1px.m │ ├── seqcfscaledsubbeta.m │ ├── seqopav.m │ ├── seqopmax.m │ ├── seqopmin.m │ ├── seqopsum.m │ ├── seqopsummaskoff.m │ ├── seqopsummaskon.m │ ├── seqsubseq.m │ └── seqwf.m │ ├── sim │ ├── runseqflatfield.m │ ├── seq2subseq.m │ ├── seqblure.m │ ├── seqfft2.m │ ├── seqflatfield.m │ ├── seqifft2.m │ ├── seqload.m │ ├── seqpadsmooth.m │ ├── seqremovemean.m │ ├── seqrewind.m │ └── seqstriperemoval.m │ ├── spotfinder │ ├── detector_locmax.m │ ├── estimator_lsq_fitquadric.m │ ├── estimator_lsq_gradintersect.m │ ├── estimator_none.m │ ├── filter_dao.m │ ├── filter_daoint.m │ ├── filter_diffav.m │ ├── filter_dog.m │ ├── filter_dogint.m │ ├── filter_gauss.m │ ├── filter_gaussint.m │ ├── filter_none.m │ ├── filter_wavelet.m │ ├── mex │ │ ├── boxmustd.cpp │ │ ├── boxmustd.mexw32 │ │ ├── boxmustd.mexw64 │ │ ├── circfilter.cpp │ │ ├── circfilter.mexw32 │ │ ├── circfilter.mexw64 │ │ ├── findlocmax2d.cpp │ │ ├── findlocmax2d.mexw32 │ │ ├── findlocmax2d.mexw64 │ │ └── listsingle.h │ ├── spotfinder.m │ ├── spotfinder_default_detector.m │ ├── spotfinder_default_estimator.m │ ├── spotfinder_default_filter.m │ ├── spotfinder_default_threshold.m │ ├── spotfinder_getnames.m │ ├── subpix2d_fitquadric.m │ ├── subpix2d_gradintersect.m │ ├── threshold_boxmustd.m │ ├── threshold_fnc.m │ ├── threshold_mustd_val.m │ ├── threshold_std_val.m │ └── threshold_val.m │ └── yaml │ ├── README │ ├── YAML.m │ └── java │ ├── LICENSE-2.0.txt │ └── snakeyaml-1.9.jar ├── SIMToolbox2.11_MATLAB ├── ReadMe.txt ├── SIMToolbox.m ├── config.m ├── configReset.m ├── license │ ├── COPYING.txt │ └── sim_logo.bmp ├── process.m ├── setEstimatePatterns.m ├── setFindPeaks.m ├── spotfinder_method_calibration.m ├── spotfinder_method_spotfinder.m └── utils │ ├── apodize │ ├── apodize_butterworth.m │ ├── apodize_circular.m │ ├── apodize_cosbell.m │ ├── apodize_gauss.m │ ├── apodize_lukosz.m │ ├── apodize_none.m │ ├── apodize_standard.m │ ├── apodize_triangle.m │ └── getapodizationnames.m │ ├── calibration │ ├── cal2Destim.cpp │ ├── cal2Destim.mexw32 │ ├── calconfig.m │ ├── calhomolin.m │ ├── calhomorad.m │ ├── cali2w.m │ ├── calload.m │ ├── calloadgdf.m │ ├── calprocess.m │ ├── calsave.m │ ├── calw2i.m │ ├── cart2sq.m │ ├── corners_detect.m │ ├── markers_check.m │ ├── markers_detect.m │ ├── markers_sort.m │ └── ptdist.m │ ├── image │ ├── fspecialseparable.m │ ├── imfilterseparable.m │ ├── imgadjust.m │ ├── imgclipval.m │ ├── imgflatfield.m │ ├── imgradprof.m │ └── imgrmpadding.m │ ├── io │ ├── cfgload.m │ ├── cfgsave.m │ ├── dimload.m │ ├── extractPathAndFilename.m │ ├── fileparts_dir.m │ ├── fileparts_name.m │ ├── fileparts_nameext.m │ ├── fixresname.m │ ├── imgdirinfo.m │ ├── imginfoinit.m │ ├── imgload.m │ ├── imgsave16.m │ ├── imgsave32.m │ ├── imgzload.m │ ├── iq2getinfo.m │ ├── iq2parse.m │ ├── isfilest.m │ ├── loadtif.m │ ├── tiffnumpg.m │ └── uigetdir_workaround.m │ ├── misc │ ├── fftInterpolate.m │ ├── imfft.m │ ├── imifft.m │ ├── lmfit1DgaussXSAO.cpp │ ├── lmfit1DgaussXSAO.mexw32 │ ├── lmfit1DgaussXSAO.mexw64 │ ├── lmfit2DgaussXYSAO.cpp │ ├── lmfit2DgaussXYSAO.mexw32 │ ├── lmfit2DgaussXYSAO.mexw64 │ ├── lmmin │ │ ├── lm_eval.c │ │ ├── lmmin.c │ │ └── lmmin.h │ ├── locmax1d.m │ ├── m2c.m │ ├── printerror.m │ ├── progressbarGUI.m │ ├── rmfields.m │ ├── sigmoid.m │ ├── sizeof.m │ ├── structcat.m │ ├── timestamp.m │ └── whichcamera.m │ ├── patterns │ ├── ptrn2camera.m │ ├── ptrnchecklines.m │ ├── ptrnclose.m │ ├── ptrndirinfo.m │ ├── ptrngetimagenames.m │ ├── ptrngetnumro.m │ ├── ptrngetnumseq.m │ ├── ptrngetro.m │ ├── ptrnload.m │ ├── ptrnmaskprecompute.m │ └── ptrnopen.m │ ├── prepareData │ ├── deg2rad.m │ ├── gen_descfile.m │ ├── gen_ptrnest.m │ ├── gen_ptrnest_orig.m │ ├── gen_repfile.m │ ├── gen_repz.m │ ├── get_ptrnimagenames.m │ └── ro_lines.m │ ├── sim-msm │ ├── MapcoreCudaFinish.mexw64 │ ├── MapcoreCudaPrepare.mexw64 │ ├── MapcoreCudaProcess.mexw64 │ ├── apodize.m │ ├── applyOTF.m │ ├── createOTF.m │ ├── estimateNoise.m │ ├── genMasks.m │ ├── imnorm.m │ ├── mapcore.m │ ├── mapsim.m │ └── spectralMask.m │ ├── sim-sr │ ├── sim_addOTF.m │ ├── sim_combine.m │ ├── sim_extract.m │ ├── sim_findpeaks.m │ ├── sim_findpeaksassign.m │ ├── sim_findpeaksloadimage.m │ ├── sim_getphase.m │ ├── sim_matchspectra.m │ └── sim_shiftspectra.m │ ├── sim-vsm │ ├── getvsmnames.m │ ├── seqcfhomodyne.m │ ├── seqcfmaskonly.m │ ├── seqcfmaxmin.m │ ├── seqcfmaxmin2av.m │ ├── seqcfscaledsub.m │ ├── seqcfscaledsub1px.m │ ├── seqcfscaledsubbeta.m │ ├── seqopav.m │ ├── seqopmax.m │ ├── seqopmin.m │ ├── seqopsum.m │ ├── seqopsummaskoff.m │ ├── seqopsummaskon.m │ ├── seqsubseq.m │ └── seqwf.m │ ├── sim │ ├── runseqflatfield.m │ ├── seq2subseq.m │ ├── seqblure.m │ ├── seqfft2.m │ ├── seqflatfield.m │ ├── seqifft2.m │ ├── seqload.m │ ├── seqpadsmooth.m │ ├── seqremovemean.m │ ├── seqrewind.m │ └── seqstriperemoval.m │ ├── spotfinder │ ├── detector_locmax.m │ ├── estimator_lsq_fitquadric.m │ ├── estimator_lsq_gradintersect.m │ ├── estimator_none.m │ ├── filter_dao.m │ ├── filter_daoint.m │ ├── filter_diffav.m │ ├── filter_dog.m │ ├── filter_dogint.m │ ├── filter_gauss.m │ ├── filter_gaussint.m │ ├── filter_none.m │ ├── filter_wavelet.m │ ├── mex │ │ ├── boxmustd.cpp │ │ ├── boxmustd.mexw32 │ │ ├── boxmustd.mexw64 │ │ ├── circfilter.cpp │ │ ├── circfilter.mexw32 │ │ ├── circfilter.mexw64 │ │ ├── findlocmax2d.cpp │ │ ├── findlocmax2d.mexw32 │ │ ├── findlocmax2d.mexw64 │ │ └── listsingle.h │ ├── spotfinder.m │ ├── spotfinder_default_detector.m │ ├── spotfinder_default_estimator.m │ ├── spotfinder_default_filter.m │ ├── spotfinder_default_threshold.m │ ├── spotfinder_getnames.m │ ├── subpix2d_fitquadric.m │ ├── subpix2d_gradintersect.m │ ├── threshold_boxmustd.m │ ├── threshold_fnc.m │ ├── threshold_mustd_val.m │ ├── threshold_std_val.m │ └── threshold_val.m │ └── yaml │ ├── README │ ├── YAML.m │ └── java │ ├── LICENSE-2.0.txt │ └── snakeyaml-1.9.jar └── SIMToolbox2.12_MATLAB ├── ReadMe.txt ├── SIMToolbox.m ├── _UPDATE_DOCUMENTATION_2.12.txt ├── config.m ├── configReset.m ├── license ├── COPYING.txt └── sim_logo.bmp ├── process.m ├── setEstimatePatterns.m ├── setFindPeaks.m ├── spotfinder_method_calibration.m ├── spotfinder_method_spotfinder.m └── utils ├── apodize ├── apodize_butterworth.m ├── apodize_circular.m ├── apodize_cosbell.m ├── apodize_gauss.m ├── apodize_lukosz.m ├── apodize_none.m ├── apodize_standard.m ├── apodize_triangle.m └── getapodizationnames.m ├── calibration ├── cal2Destim.cpp ├── cal2Destim.mexw32 ├── calconfig.m ├── calhomolin.m ├── calhomorad.m ├── cali2w.m ├── calload.m ├── calloadgdf.m ├── calprocess.m ├── calsave.m ├── calw2i.m ├── cart2sq.m ├── corners_detect.m ├── markers_check.m ├── markers_detect.m ├── markers_sort.m └── ptdist.m ├── image ├── fspecialseparable.m ├── imfilterseparable.m ├── imgadjust.m ├── imgclipval.m ├── imgflatfield.m ├── imgradprof.m └── imgrmpadding.m ├── io ├── cfgload.m ├── cfgsave.m ├── dimload.m ├── extractPathAndFilename.m ├── fileparts_dir.m ├── fileparts_name.m ├── fileparts_nameext.m ├── fixresname.m ├── imgdirinfo.m ├── imginfoinit.m ├── imgload.m ├── imgsave16.m ├── imgsave32.m ├── imgzload.m ├── iq2getinfo.m ├── iq2parse.m ├── isfilest.m ├── loadtif.m ├── tiffnumpg.m └── uigetdir_workaround.m ├── misc ├── colormaps │ ├── isolum.m │ ├── jetwhite.m │ └── morgenstemning.m ├── fftInterpolate.m ├── imfft.m ├── imifft.m ├── lmfit1DgaussXSAO.cpp ├── lmfit1DgaussXSAO.mexw32 ├── lmfit1DgaussXSAO.mexw64 ├── lmfit2DgaussXYSAO.cpp ├── lmfit2DgaussXYSAO.mexw32 ├── lmfit2DgaussXYSAO.mexw64 ├── lmmin │ ├── lm_eval.c │ ├── lmmin.c │ └── lmmin.h ├── locmax1d.m ├── m2c.m ├── onoff.m ├── printerror.m ├── progressbarGUI.m ├── rmfields.m ├── sigmoid.m ├── sizeof.m ├── structcat.m ├── timestamp.m └── whichcamera.m ├── patterns ├── ptrn2camera.m ├── ptrnchecklines.m ├── ptrnclose.m ├── ptrndirinfo.m ├── ptrngetimagenames.m ├── ptrngetnumro.m ├── ptrngetnumseq.m ├── ptrngetro.m ├── ptrnload.m ├── ptrnmaskprecompute.m └── ptrnopen.m ├── prepareData ├── deg2rad.m ├── gen_descfile.m ├── gen_ptrnest.m ├── gen_ptrnest_orig.m ├── gen_repfile.m ├── gen_repz.m ├── get_ptrnimagenames.m └── ro_lines.m ├── sim-msm ├── MapcoreCudaFinish.mexw64 ├── MapcoreCudaPrepare.mexw64 ├── MapcoreCudaProcess.mexw64 ├── apodize.m ├── applyOTF.m ├── createOTF.m ├── estimateNoise.m ├── genMasks.m ├── imnorm.m ├── mapcore.m ├── mapsim.m └── spectralMask.m ├── sim-sr ├── sim_addOTF.m ├── sim_combine.m ├── sim_extract.m ├── sim_findpeaks.m ├── sim_findpeaksassign.m ├── sim_findpeaksloadimage.m ├── sim_getphase.m ├── sim_matchspectra.m └── sim_shiftspectra.m ├── sim-vsm ├── getvsmnames.m ├── seqbgsubtract.m ├── seqcfhomodyne.m ├── seqcfmaskonly.m ├── seqcfmaxmin.m ├── seqcfmaxmin2av.m ├── seqcfscaledsub.m ├── seqcfscaledsub1px.m ├── seqcfscaledsubbeta.m ├── seqopav.m ├── seqopmax.m ├── seqopmin.m ├── seqopsum.m ├── seqopsummaskoff.m ├── seqopsummaskon.m ├── seqsubseq.m └── seqwf.m ├── sim ├── runseqflatfield.m ├── seq2subseq.m ├── seqblure.m ├── seqfft2.m ├── seqflatfield.m ├── seqifft2.m ├── seqload.m ├── seqpadsmooth.m ├── seqremovemean.m ├── seqrewind.m └── seqstriperemoval.m ├── spotfinder ├── detector_locmax.m ├── estimator_lsq_fitquadric.m ├── estimator_lsq_gradintersect.m ├── estimator_none.m ├── filter_dao.m ├── filter_daoint.m ├── filter_diffav.m ├── filter_dog.m ├── filter_dogint.m ├── filter_gauss.m ├── filter_gaussint.m ├── filter_none.m ├── filter_wavelet.m ├── mex │ ├── boxmustd.cpp │ ├── boxmustd.mexw32 │ ├── boxmustd.mexw64 │ ├── circfilter.cpp │ ├── circfilter.mexw32 │ ├── circfilter.mexw64 │ ├── findlocmax2d.cpp │ ├── findlocmax2d.mexw32 │ ├── findlocmax2d.mexw64 │ └── listsingle.h ├── spotfinder.m ├── spotfinder_default_detector.m ├── spotfinder_default_estimator.m ├── spotfinder_default_filter.m ├── spotfinder_default_threshold.m ├── spotfinder_getnames.m ├── subpix2d_fitquadric.m ├── subpix2d_gradintersect.m ├── threshold_boxmustd.m ├── threshold_fnc.m ├── threshold_mustd_val.m ├── threshold_std_val.m └── threshold_val.m └── yaml ├── README ├── YAML.m └── java ├── LICENSE-2.0.txt └── snakeyaml-1.9.jar /SIMToolbox1.10_MATLAB/SIMToolbox.m: 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