< Master index Index for CellSort 1.2 >

Index for CellSort 1.2

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).
  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: CellsortPlotPCspectrumCellsortPlotPCspectrum(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: CellsortICAplotCellsortICAplot(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:CellsortApplyFiltercell_sig = CellsortApplyFilter(fn, ica_segments, flims, movm, subtractmean)
  Step 5:CellsortFindspikes[spmat, spt, spc, zsig] = CellsortFindspikes(ica_sig, thresh, dt, deconvtau, normalization)


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