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Automated analysis of "puffs" receptor recycling movies, based on Danuser lab's cmeAnalysis code.

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GPL-3.0, BSD-2-Clause licenses found

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GPL-3.0
GPL-License.txt
BSD-2-Clause
inpaint_nans_license.txt
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weinberz/puffsAnalysis

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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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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

Copyright © T. Phan & Z. Weinberg 2016

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Automated analysis of "puffs" receptor recycling movies, based on Danuser lab's cmeAnalysis code.

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Readme

License

GPL-3.0, BSD-2-Clause licenses found

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GPL-3.0
GPL-License.txt
BSD-2-Clause
inpaint_nans_license.txt
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