Index for CellSort 1.0

Index for CellSort 1.0

Matlab files in this directory:

CellSort is a MATLAB toolbox containing code that accompanies the manuscript, Automated analysis of cellular signals from large-scale calcium imaging data by Eran Mukamel, Axel Nimmerjahn and Mark Schnitzer, NEURON (2009). Please address comments and questions to Eran Mukamel (eran at post dot harvard dot edu) or Mark Schnitzer (mschnitz at stanford dot edu).

Step 1: CellsortPCA	[mixedsig, mixedfilters, CovEvals, covtrace, movm, movtm] = CellsortPCA(fn, flims, nPCs, dsamp, outputdir, badframes)
Step 2a: CellsortChoosePCs	[PCuse] = CellsortChoosePCs(fn, mixedfilters)
Step 2b: CellsortPlotPCspectrum	CellsortPlotPCspectrum(fn, CovEvals, pcuse)
Step 3a: CellsortICA	[ica_sig, ica_filters, ica_A, numiter] = CellsortICA(mixedsig, mixedfilters, PCuse, mu, nIC, ica_A_guess, termtol, maxrounds)
Step 3b: CellsortICAplot	CellsortICAplot(mode, ica_filters, ica_sig, f0, tlims, dt, ratebin, plottype, ICuse, spt, spc)
Step 4a: CellsortSegmentation	[ica_segments, segmentlabel, segcentroid] = CellsortSegmentation(ica_filters, smwidth, thresh, arealims, plotting)
Step 4b:CellsortApplyFilter	cell_sig = CellsortApplyFilter(fn, ica_segments, flims, movm, subtractmean)
Step 5:CellsortFindspikes	[spmat, spt, spc, zsig] = CellsortFindspikes(ica_sig, thresh, dt, deconvtau, normalization)