GitHub - weinberz/puffsAnalysis: Automated analysis of "puffs" receptor recycling movies, based on Danuser lab's cmeAnalysis code.

Analysis package for evaluating TIR-FM movies of GPCR recycling. Primarily based on detection and tracking code in cmeAnalysis (originally published in Aguet et al. 2013 and available from the Danuser Lab or in a modified form here).

Classification requires the following Python packages (all available from pip):

numpy
scipy
sklearn
h5py
matplotlib

Name		Name	Last commit message	Last commit date
Latest commit History 115 Commits
PointSourceDetection		PointSourceDetection
mex		mex
.gitattributes		.gitattributes
GPL-License.txt		GPL-License.txt
README.md		README.md
adtest1.m		adtest1.m
asymDeterm2D3D.m		asymDeterm2D3D.m
autoSVM.m		autoSVM.m
barplot2.m		barplot2.m
binarySegmentLengths.m		binarySegmentLengths.m
coordAmpMatFromIndicesSparse.m		coordAmpMatFromIndicesSparse.m
costMatLinearMotionCloseGaps2.m		costMatLinearMotionCloseGaps2.m
costMatLinearMotionLink2.m		costMatLinearMotionLink2.m
countTracks.m		countTracks.m
cutTrack.m		cutTrack.m
densityplot.m		densityplot.m
detectEDFOutliers.m		detectEDFOutliers.m
estimTrackTypeParamLM2.m		estimTrackTypeParamLM2.m
extractComplexData.m		extractComplexData.m
extractComplexNonPuffData.m		extractComplexNonPuffData.m
extractComplexPuffData.m		extractComplexPuffData.m
extractPuffData.m		extractPuffData.m
fallFit.m		fallFit.m
featureRequests		featureRequests
filterGauss1D.m		filterGauss1D.m
filterGauss2D.m		filterGauss2D.m
findTrackGaps.m		findTrackGaps.m
fitExpToHist.m		fitExpToHist.m
fitGaussianModeToCDF.m		fitGaussianModeToCDF.m
fitGaussianModeToHist.m		fitGaussianModeToHist.m
formatTickLabels.m		formatTickLabels.m
g4pLifetimeHistogram.m		g4pLifetimeHistogram.m
gaussian_kde.py		gaussian_kde.py
getAveDispEllipseAll2.m		getAveDispEllipseAll2.m
getCellDir.m		getCellDir.m
getCellMask.m		getCellMask.m
getDirFromPath.m		getDirFromPath.m
getExpDir.m		getExpDir.m
getFluorPropStruct.m		getFluorPropStruct.m
getFluorophoreHues.m		getFluorophoreHues.m
getGaussianFits.m		getGaussianFits.m
getGaussianPSFsigma.m		getGaussianPSFsigma.m
getGaussianPSFsigmaFromData.m		getGaussianPSFsigmaFromData.m
getLifetimeData.m		getLifetimeData.m
getLifetimeHistogram.m		getLifetimeHistogram.m
getMovieName.m		getMovieName.m
getPSNRDistribution.m		getPSNRDistribution.m
getParentDir.m		getParentDir.m
getRGBindex.m		getRGBindex.m
getShortPath.m		getShortPath.m
getTrackSEL.m		getTrackSEL.m
getTrackStackStandalone.m		getTrackStackStandalone.m
getVisitorIndex.m		getVisitorIndex.m
ginputx.m		ginputx.m
histogram.m		histogram.m
inpaint_nans.m		inpaint_nans.m
inpaint_nans_license.txt		inpaint_nans_license.txt
intensityAnalysis.m		intensityAnalysis.m
kalmanGainLinearMotion.m		kalmanGainLinearMotion.m
kalmanInitLinearMotion.m		kalmanInitLinearMotion.m
kalmanResMemLM.m		kalmanResMemLM.m
kalmanReverseLinearMotion.m		kalmanReverseLinearMotion.m
lap.m		lap.m
latA.csv		latA.csv
linkFeaturesKalmanSparse.m		linkFeaturesKalmanSparse.m
listSelectGUI.fig		listSelectGUI.fig
listSelectGUI.m		listSelectGUI.m
loadConditionData.m		loadConditionData.m
loadFigureSettings.m		loadFigureSettings.m
loadTrackSettings.m		loadTrackSettings.m
loadTracks.m		loadTracks.m
locmax1d.m		locmax1d.m
locmin1d.m		locmin1d.m
map.md		map.md
maskFromFirstMode.m		maskFromFirstMode.m
mat2py.py		mat2py.py
mat_handler.py		mat_handler.py
methods_of_inpaint_nans.m		methods_of_inpaint_nans.m
name2wavelength.m		name2wavelength.m
novel_data.csv		novel_data.csv
paper.ipynb		paper.ipynb
pitcountAnalysis.m		pitcountAnalysis.m
plotCCPCDF.m		plotCCPCDF.m
plotIntensityCohorts.m		plotIntensityCohorts.m
plotLifetimeComparison.m		plotLifetimeComparison.m
plotLifetimeComparison1Ch.m		plotLifetimeComparison1Ch.m
plotLifetimes.m		plotLifetimes.m
plotMaxIntVsLifetime.m		plotMaxIntVsLifetime.m
plotMaxIntensityDistribution.m		plotMaxIntensityDistribution.m
plotPSNRDistribution.m		plotPSNRDistribution.m
plotRandomForests.py		plotRandomForests.py
plotTrack.m		plotTrack.m
plotTrackAndMontage.m		plotTrackAndMontage.m
plotTrackClasses.m		plotTrackClasses.m
plotTrackMontage.m		plotTrackMontage.m
plot_ccp_cdf.m		plot_ccp_cdf.m
plot_slave_cdf.m		plot_slave_cdf.m
progressText.m		progressText.m
puffChecker.m		puffChecker.m
puffScorer.m		puffScorer.m

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weinberz/puffsAnalysis

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