├── +svdVid ├── UDPCallback.m └── listen.m ├── .gitignore ├── LICENSE ├── README.md ├── core ├── HemoCorrectLocal.m ├── HemoCorrectNonlocal.m ├── alignToTarget.m ├── align_iterative.m ├── determineTargetFrame.m ├── dffFromSVD.m ├── eventLockedAvgSVD.m ├── generateRegistrationTarget.m ├── get_svdcomps.m ├── loadRawToDat.m ├── pick_reg_init.m ├── quickHemoCorrect.m ├── reSVD.M ├── registerDatFile.m ├── register_movie.m ├── registration_offsets.m ├── sparseRetinotopy.m ├── svdVideoObj.m ├── tifToDat.m └── timeFromPCOBinaryMulti.m ├── generalUtils ├── ChangeU.m ├── SubSampleShift.m ├── binImage.m ├── determineTimelineAlignments.m ├── detrendAndFilt.m ├── fileHandling │ ├── LoadCustomPCO.m │ ├── generateFileList.m │ ├── loadTiffStack.m │ ├── pathForThisOS.m │ ├── readB16.m │ ├── readOneCustomPCO.m │ ├── readUVforExp.m │ ├── readUfromNPY.m │ ├── readVfromNPY.m │ └── writeUVtoNPY.m ├── findNearestPoint.m ├── getNFramesFromCustomPCOFiles.m ├── getNFramesFromTifFiles.m ├── getStrobeTimes.m ├── hpFilt.m ├── mailFromLugaro.m ├── mergeStructs.m ├── plotting │ ├── colormap_BlueWhiteRed.m │ ├── colormap_RedWhiteBlue.m │ ├── colormap_blueblackred.m │ ├── colormap_redblackblue.m │ ├── makepretty.m │ ├── plotMJ2frame.m │ ├── rasterize.m │ └── subtightplot.m ├── quickLoadUVt.m ├── removeStamps.m ├── rotateImages.m ├── schmitt.m ├── schmittTimes.m └── svdFrameReconstruct.m ├── miniGUIs ├── frameGen_divide.m ├── helpers │ ├── prepareAuxVids.m │ └── prepareTimelineTraces.m ├── movieWithTracesSVD.m ├── movieWithTracesSVDmulti.m ├── pixelCorrelationViewer.m ├── pixelCorrelationViewerSVD.m ├── pixelTuningCurveViewer.m ├── pixelTuningCurveViewerSVD.m ├── quickMovieWithVids.m ├── svdViewer.m └── transformationViewerSVD.m ├── regression ├── kernelRegression.m ├── kernelRegression2.m ├── kernelRegression3.m ├── makeContPredictor.m ├── makeKernelRegPredictor.m ├── makeKernelRegPredictorCos.m └── makeKernelRegPredictorExp.m └── scripts ├── lugaro_daily_pipeline.m ├── pipelineHere.m ├── pipelineHereKT.m ├── pipelineScript.m ├── saveSVD.m ├── setSVDParams.m ├── svdConfig.m ├── svdROI.m └── tests ├── imageRegTestScript.m └── speedcomp.m /+svdVid/UDPCallback.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/+svdVid/UDPCallback.m -------------------------------------------------------------------------------- /+svdVid/listen.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/+svdVid/listen.m -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *.asv 2 | mySetSVDparams.m 3 | .DS_Store 4 | *.m~ -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/README.md -------------------------------------------------------------------------------- /core/HemoCorrectLocal.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/HemoCorrectLocal.m -------------------------------------------------------------------------------- /core/HemoCorrectNonlocal.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/HemoCorrectNonlocal.m -------------------------------------------------------------------------------- /core/alignToTarget.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/alignToTarget.m -------------------------------------------------------------------------------- /core/align_iterative.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/align_iterative.m -------------------------------------------------------------------------------- /core/determineTargetFrame.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/determineTargetFrame.m -------------------------------------------------------------------------------- /core/dffFromSVD.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/dffFromSVD.m -------------------------------------------------------------------------------- /core/eventLockedAvgSVD.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/eventLockedAvgSVD.m -------------------------------------------------------------------------------- /core/generateRegistrationTarget.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/generateRegistrationTarget.m -------------------------------------------------------------------------------- /core/get_svdcomps.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/get_svdcomps.m -------------------------------------------------------------------------------- /core/loadRawToDat.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/loadRawToDat.m -------------------------------------------------------------------------------- /core/pick_reg_init.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/pick_reg_init.m -------------------------------------------------------------------------------- /core/quickHemoCorrect.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/quickHemoCorrect.m -------------------------------------------------------------------------------- /core/reSVD.M: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/reSVD.M -------------------------------------------------------------------------------- /core/registerDatFile.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/registerDatFile.m -------------------------------------------------------------------------------- /core/register_movie.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/register_movie.m -------------------------------------------------------------------------------- /core/registration_offsets.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/registration_offsets.m -------------------------------------------------------------------------------- /core/sparseRetinotopy.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/sparseRetinotopy.m -------------------------------------------------------------------------------- /core/svdVideoObj.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/svdVideoObj.m -------------------------------------------------------------------------------- /core/tifToDat.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/tifToDat.m -------------------------------------------------------------------------------- /core/timeFromPCOBinaryMulti.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/core/timeFromPCOBinaryMulti.m -------------------------------------------------------------------------------- /generalUtils/ChangeU.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/ChangeU.m -------------------------------------------------------------------------------- /generalUtils/SubSampleShift.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/SubSampleShift.m -------------------------------------------------------------------------------- /generalUtils/binImage.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/binImage.m -------------------------------------------------------------------------------- /generalUtils/determineTimelineAlignments.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/determineTimelineAlignments.m -------------------------------------------------------------------------------- /generalUtils/detrendAndFilt.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/detrendAndFilt.m -------------------------------------------------------------------------------- /generalUtils/fileHandling/LoadCustomPCO.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/fileHandling/LoadCustomPCO.m -------------------------------------------------------------------------------- /generalUtils/fileHandling/generateFileList.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/fileHandling/generateFileList.m -------------------------------------------------------------------------------- /generalUtils/fileHandling/loadTiffStack.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/fileHandling/loadTiffStack.m -------------------------------------------------------------------------------- /generalUtils/fileHandling/pathForThisOS.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/fileHandling/pathForThisOS.m -------------------------------------------------------------------------------- /generalUtils/fileHandling/readB16.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/fileHandling/readB16.m -------------------------------------------------------------------------------- /generalUtils/fileHandling/readOneCustomPCO.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/fileHandling/readOneCustomPCO.m -------------------------------------------------------------------------------- /generalUtils/fileHandling/readUVforExp.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/fileHandling/readUVforExp.m -------------------------------------------------------------------------------- /generalUtils/fileHandling/readUfromNPY.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/fileHandling/readUfromNPY.m -------------------------------------------------------------------------------- /generalUtils/fileHandling/readVfromNPY.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/fileHandling/readVfromNPY.m -------------------------------------------------------------------------------- /generalUtils/fileHandling/writeUVtoNPY.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/fileHandling/writeUVtoNPY.m -------------------------------------------------------------------------------- /generalUtils/findNearestPoint.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/findNearestPoint.m -------------------------------------------------------------------------------- /generalUtils/getNFramesFromCustomPCOFiles.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/getNFramesFromCustomPCOFiles.m -------------------------------------------------------------------------------- /generalUtils/getNFramesFromTifFiles.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/getNFramesFromTifFiles.m -------------------------------------------------------------------------------- /generalUtils/getStrobeTimes.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/getStrobeTimes.m -------------------------------------------------------------------------------- /generalUtils/hpFilt.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/hpFilt.m -------------------------------------------------------------------------------- /generalUtils/mailFromLugaro.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/mailFromLugaro.m -------------------------------------------------------------------------------- /generalUtils/mergeStructs.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/mergeStructs.m -------------------------------------------------------------------------------- /generalUtils/plotting/colormap_BlueWhiteRed.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/plotting/colormap_BlueWhiteRed.m -------------------------------------------------------------------------------- /generalUtils/plotting/colormap_RedWhiteBlue.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/plotting/colormap_RedWhiteBlue.m -------------------------------------------------------------------------------- /generalUtils/plotting/colormap_blueblackred.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/plotting/colormap_blueblackred.m -------------------------------------------------------------------------------- /generalUtils/plotting/colormap_redblackblue.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/plotting/colormap_redblackblue.m -------------------------------------------------------------------------------- /generalUtils/plotting/makepretty.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/plotting/makepretty.m -------------------------------------------------------------------------------- /generalUtils/plotting/plotMJ2frame.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/plotting/plotMJ2frame.m -------------------------------------------------------------------------------- /generalUtils/plotting/rasterize.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/plotting/rasterize.m -------------------------------------------------------------------------------- /generalUtils/plotting/subtightplot.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/plotting/subtightplot.m -------------------------------------------------------------------------------- /generalUtils/quickLoadUVt.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/quickLoadUVt.m -------------------------------------------------------------------------------- /generalUtils/removeStamps.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/removeStamps.m -------------------------------------------------------------------------------- /generalUtils/rotateImages.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/rotateImages.m -------------------------------------------------------------------------------- /generalUtils/schmitt.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/schmitt.m -------------------------------------------------------------------------------- /generalUtils/schmittTimes.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/schmittTimes.m -------------------------------------------------------------------------------- /generalUtils/svdFrameReconstruct.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/generalUtils/svdFrameReconstruct.m -------------------------------------------------------------------------------- /miniGUIs/frameGen_divide.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/miniGUIs/frameGen_divide.m -------------------------------------------------------------------------------- /miniGUIs/helpers/prepareAuxVids.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/miniGUIs/helpers/prepareAuxVids.m -------------------------------------------------------------------------------- /miniGUIs/helpers/prepareTimelineTraces.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/miniGUIs/helpers/prepareTimelineTraces.m -------------------------------------------------------------------------------- /miniGUIs/movieWithTracesSVD.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/miniGUIs/movieWithTracesSVD.m -------------------------------------------------------------------------------- /miniGUIs/movieWithTracesSVDmulti.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/miniGUIs/movieWithTracesSVDmulti.m -------------------------------------------------------------------------------- /miniGUIs/pixelCorrelationViewer.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/miniGUIs/pixelCorrelationViewer.m -------------------------------------------------------------------------------- /miniGUIs/pixelCorrelationViewerSVD.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/miniGUIs/pixelCorrelationViewerSVD.m -------------------------------------------------------------------------------- /miniGUIs/pixelTuningCurveViewer.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/miniGUIs/pixelTuningCurveViewer.m -------------------------------------------------------------------------------- /miniGUIs/pixelTuningCurveViewerSVD.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/miniGUIs/pixelTuningCurveViewerSVD.m -------------------------------------------------------------------------------- /miniGUIs/quickMovieWithVids.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/miniGUIs/quickMovieWithVids.m -------------------------------------------------------------------------------- /miniGUIs/svdViewer.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/miniGUIs/svdViewer.m -------------------------------------------------------------------------------- /miniGUIs/transformationViewerSVD.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/miniGUIs/transformationViewerSVD.m -------------------------------------------------------------------------------- /regression/kernelRegression.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/regression/kernelRegression.m -------------------------------------------------------------------------------- /regression/kernelRegression2.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/regression/kernelRegression2.m -------------------------------------------------------------------------------- /regression/kernelRegression3.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/regression/kernelRegression3.m -------------------------------------------------------------------------------- /regression/makeContPredictor.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/regression/makeContPredictor.m -------------------------------------------------------------------------------- /regression/makeKernelRegPredictor.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/regression/makeKernelRegPredictor.m -------------------------------------------------------------------------------- /regression/makeKernelRegPredictorCos.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/regression/makeKernelRegPredictorCos.m -------------------------------------------------------------------------------- /regression/makeKernelRegPredictorExp.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/regression/makeKernelRegPredictorExp.m -------------------------------------------------------------------------------- /scripts/lugaro_daily_pipeline.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/scripts/lugaro_daily_pipeline.m -------------------------------------------------------------------------------- /scripts/pipelineHere.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/scripts/pipelineHere.m -------------------------------------------------------------------------------- /scripts/pipelineHereKT.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/scripts/pipelineHereKT.m -------------------------------------------------------------------------------- /scripts/pipelineScript.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/scripts/pipelineScript.m -------------------------------------------------------------------------------- /scripts/saveSVD.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/scripts/saveSVD.m -------------------------------------------------------------------------------- /scripts/setSVDParams.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/scripts/setSVDParams.m -------------------------------------------------------------------------------- /scripts/svdConfig.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/scripts/svdConfig.m -------------------------------------------------------------------------------- /scripts/svdROI.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/scripts/svdROI.m -------------------------------------------------------------------------------- /scripts/tests/imageRegTestScript.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/scripts/tests/imageRegTestScript.m -------------------------------------------------------------------------------- /scripts/tests/speedcomp.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cortex-lab/widefield/HEAD/scripts/tests/speedcomp.m --------------------------------------------------------------------------------