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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2

CreateReadme.m
  SCRIPT DETAILS: A script to collect help descriptions from a directory (with subdirectories) of m-files.
  

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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/AlignTimeSeries

TNC_AlignRasters.m
  FUNCTION DETAILS: Using a set of timestamps provided in ALIGNSTAMPS creates a matrix of DATA vectors that span -WINDOW(1,1) to +WINDOW(1,2) around each timestamp.
  
TNC_AlignedMatrix.m
  FUNCTION DETAILS: For each channel create a field in the structure 'alignedMatrix' that has an matrix of SPIKETIMES aligned to the list of EVENTIMES passed in and that extends from -WINDOW(1,1) to WINDOW(1,2) with SAMPLING precision
  
TNC_SmoothAlignedRaster.m
TNC


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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/BehaviorHeadStage

TNC_BHS_ApproachTrajectories.m
  Script for analysis of behavior headstage data: TNC



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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/CreateFunctions

TNC_CreateCausalKernel.m

TNC_CreateGaussian.m
  FUNCTION DETAILS: 
  
TNC_CreateRBColormap.m
  FUNCTION DETAILS: Simple utility to create a RWB style color map
  
TNC_CreateReMapMatrix.m
  FUNCTION DETAILS: Create a matrix of correct channel indexes in sequence. Using this function a user can generate an ordered list of remappings that can be used in visualization functions.
  


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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/DataLoading

LoadCSVdataScript.m

TNC_BuildSegsFromMemory.m
  FUNCTION DETAILS: This function goes through a list of events and retrieves windowed segments from continuous recordings already loaded into memory (generally this is designed to work for smaller file sizes).
  
TNC_ConvertSortedNEVtoDDS.m
  FUNCTION DETAILS: Convert an NEV file with sorted spikes to the DudmanLabDataStructure (DDS)
  
TNC_ConvertSortedNEXtoDDS.m
  FUNCTION DETAILS: Convert an NEV file with sorted spikes to the DudmanLabDataStructure (DDS)
  
TNC_ConvertTSDtoPopData.m
TNC
TNC_ExtractContBehavData.m
TNC
TNC_GetDigitalStampsNEX.m
  FUNCTION DETAILS: Digital stamps need to be extracted somewhat differently from the nex and nev files. This is a utility function to assist with that.
  
TNC_LoadData.m
  FUNCTION DETAILS: Function that loads multiple data formats into TONIC; Can load: Blackrock, MAT structures; FUTURE SUPPORT: Neuralynx, Plexon?, APIG, NeuroExplorer, OFS
  
TNC_PackBlackrockSession.m
  FUNCTION DETAILS: Load and pack a given session of Blackrock Data into a single standard structure organization
  
TNC_ReadContDataSeg.m
  FUNCTION DETAILS: grabs segments of continuous data from large multichannel continuous recording data
  
TNC_ReadSeqHeader.m
  [seq
TNC_ReadSeqImages.m
  seq
gid2gnImport.m

tnc_f_importGid2Gnfile.m
 IMPORTFILE Import numeric data from a text file as a matrix.
    GID2GN = IMPORTFILE(FILENAME) Reads data from text file FILENAME for
    the default selection.
 
    GID2GN = IMPORTFILE(FILENAME, STARTROW, ENDROW) Reads data from rows
    STARTROW through ENDROW of text file FILENAME.
 
  Example:
    gid2gn = tnc


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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/DataWriting

TNC_CompressImageArray.m

TNC_ExportMatToIgor.m
TNC
TNC_ExportRasterToIgor.m
TNC
TNC_PhotoStimToStruct.m
  FUNCTION DETAILS: High level function that builds a single structure containing a standard set of analyses for every unit
  
TNC_U_PackH5ExperimentFile.m
TNC


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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/EventDetectionClassification

TNC_AddCluster.m
TNC
TNC_EventAlign.m
  FUNCTION DETAILS: align detected events using interpolation to find the threshold crossing accurately.
  
TNC_EventClean.m
  FUNCTION DETAILS: a function that provides indices for identified events based upon a generated heuristic function.
  
TNC_EventCluster.m
  FUNCTION DETAILS: Performs the clustering (elsewhere called 'classification') step where individual events are given integer ids as members of particular clusters. Further a confidence value is also returned that provides a metric for the distance of each event from the center of the cluster of which it is a member.
  
TNC_EventDetect.m

TNC_EventExtract.m

TNC_EventExtractME.m

TNC_EventHeuristic.m
  FUNCTION DETAILS: test the thresholded event data for quality based upon a heuristic that examines the spectral density of the events by projecting events onto a wavelet or sinc function.
  
TNC_EventQuant.m
  FUNCTION DETAILS: For a set of discrete events measure the "distance" between each event and a "target" waveform. Distances and targets are chosen to maximize the "clusterability" of the waveforms for subsequent steps. In many cases multiple targets and distance metrics should be used. See the help for details on supported targets and distance metrics.
  
TNC_EventQuantME.m

TNC_EventQuantSE.m
  Copyright (C) 2015 by Howard Hughes Medical Institute.
 
  FUNCTION DETAILS: For a set of discrete events measure the "distance" between each event and a "target" waveform. Distances and targets are chosen to maximize the "clusterability" of the waveforms for subsequent steps. In many cases multiple targets and distance metrics should be used. See the help for details on supported targets and distance metrics.
  
TNC_EventReconcile.m
  FUNCTION DETAILS: This function takes in events detected on individual channels and seeks to reconcile all events such that at any moment in time only a single event occurs on a given electrode grouping. The default behavior is to take the channel on which the event with the largest amplitude occurs as the 'reference time' for the event.
  
TNC_ExtractLFP.m

TNC_FilterData2.m
  FUNCTION DETAILS: general utility to separate data into a pair of bandwidths for spike sorting and continuous analysis. LowBand is 2-0.1k; HiBand: 0.7k-7k
  
TNC_FindArtifacts.m
TNC
TNC_FindEventsInContData.m
TNC
TNC_MergeClusters.m
TNC
TNC_RmEvents.m
TNC
TNC_SSPL_ConvertNEVtoFeatures.m

TNC_SSPL_CreateAnalysisConfigFile.m
  TNC
TNC_SSPL_EventDetect.m
  FUNCTION DETAILS: This function goes through a single channel of filtered recording data and looks for threshold crossings. A second stage then tests these threshold crossings according to a template matching heuristic to try to classify significant events.
  
TNC_SSPL_EventDetectME.m
  FUNCTION DETAILS: This function goes through a single channel of filtered recording data and looks for threshold crossings. A second stage then tests these threshold crossings according to a template matching heuristic to try to classify significant events.
  
TNC_SSPL_EventDetectSW.m
  FUNCTION DETAILS: This function goes through a single channel of filtered recording data and looks for threshold crossings. A second stage then tests these threshold crossings according to a template matching heuristic to try to classify significant events.
  
TNC_SSPL_EventExtract.m

TNC_SSPL_EventExtractME.m
  FUNCTION DETAILS: This function goes through a single channel of filtered recording data and looks for threshold crossings. A second stage then tests these threshold crossings according to a template matching heuristic to try to classify significant events.
  
TNC_SSPL_EventQuantME.m
  FUNCTION DETAILS: 
  
TNC_SSPL_EventQuantSE.m
  Copyright (C) 2015 by Howard Hughes Medical Institute.
 
  FUNCTION DETAILS: For a set of discrete events measure the "distance" between each event and a "target" waveform. Distances and targets are chosen to maximize the "clusterability" of the waveforms for subsequent steps. In many cases multiple targets and distance metrics should be used. See the help for details on supported targets and distance metrics.
  
TNC_SSPL_ExtendManualSort.m
  
TNC_SSPL_ExtendOnlineSort.m
  
TNC_SSPL_Features.m
  
TNC_SSPL_Features_v2.m
  
TNC_SSPL_NevPreviewer.m

TNC_SSPL_Ns5Previewer.m

TNC_SSPL_SingleSite.m

TNC_SSPL_cluster_dp.m

TNC_SSP_ConvertNEVtoFeatures.m

TNC_SSP_ExtractFeatures.m

TNC_SSP_SingleSite.m

TNC_SSpipe.m



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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/ExternalPackages

angleDiff.m

getReachTimes.m

moveavg.m
 MOVING
normalizeAngle.m

rasterplot.m

violin.m
 
wmean.m



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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/ExtractFunctions

ExtractPopulationDataScript.m

TNC_ContTrigWins.m

TNC_EventExtractImage.m
  FUNCTION DETAILS: This function goes through a single channel of filtered recording data and looks for threshold crossings. A second stage then tests these threshold crossings according to a template matching heuristic to try to classify significant events.
  
TNC_ExtTrigWins.m
TNC
TNC_ExtractContTrigWinMUA.m
  Show MUA for a given electrode using ContTrigWin data
  DEPENDENCY:
      PRE-analyzed with TNC
TNC_ExtractImageAlignment.m
TNC
TNC_ExtractMovement.m
  FUNCTION DETAILS: Simple function to try and extract movement in a compressed or uncompressed image array loaded into memory.
  
TNC_ExtractNEV2IndChan.m
TNC
TNC_ExtractPeaks.m
  detect
TNC_ExtractTrajectories.m
  FUNCTION OVERVIEW: Extract arm movement trajectories from resistive analog sensor
  
TNC_FilterData.m
  FUNCTION DETAILS: general utility to separate data into a pair of bandwidths for spike sorting and continuous analysis. LowBand is 2-0.1k; HiBand: 0.5k-7.2k
  
TNC_FindOnsets.m
TNC
TNC_ImgStackMode.m
TNC
wavefilter.m



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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/HighPerformanceComputing

TNC_HPC_MergeMatFiles.m

TNC_HPC_ShowGMSolution.m



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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/MixtureModel

TNC_MM_AlignClassLabels.m

TNC_MM_BestNumComponents.m

TNC_MM_CrossValidation.m

TNC_MM_ElectrodeCoordinates.m

TNC_MM_GaussMixLogLikelihood.m

TNC_MM_InitialGuess.m

TNC_MM_Means2XYZ.m

TNC_MM_SortSpikes.m

TNC_MM_SummarizeResults.m
TNC
TNC_MM_Triangulation.m

TNC_MM_UpdateNeuroCube.m



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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/NeuroCube

Manual_neuron.m
Manual
Rotate_coordinates.m

Update_auto.m
Update
Update_neurons.m

Update_plot.m

Update_progress.m

Update_text_boxes.m

addpaths.m

calculate_ampl_spike.m

calculate_ampl_spike1.m

calculate_ampl_spike2.m

filledCircle.m

filt_elec.m

get_phi1.m

neurocube.m
  neurocube M-file for neurocube.fig
       neurocube, by itself, creates a new neurocube or raises the existing
       singleton*.
 
       H = neurocube returns the handle to a new neurocube or the handle to
       the existing singleton*.
 
       neurocube('CALLBACK',hObject,eventData,handles,...) calls the local
       function named CALLBACK in neurocube.M with the given input arguments.
 
       neurocube('Property','Value',...) creates a new neurocube or raises the
       existing singleton*.  Starting from the left, property value pairs are
       applied to the GUI before neurocube
normalize_spike_shape.m

normalize_spike_shape2.m

run_simulation.m

test_read_text.m
  Example: 
  >> test


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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/ObjectOrientedProgramming

TNC_OOP_FeatureExtractionInputParser.m
  Copyright (C) 2015 by Howard Hughes Medical Institute.
 

    Reference page in Doc Center
       doc TNC
TNC_OOP_SpikeSortingInputParser.m
  Copyright (C) 2015 by Howard Hughes Medical Institute.
 

    Reference page in Doc Center
       doc TNC
TNC_OOP_Spikes.m
  Copyright (C) 2015 by Howard Hughes Medical Institute.
 

    Reference page in Doc Center
       doc TNC


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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/Quantification

TNC_BinAndMean.m
TNC
TNC_BoxcarAverage.m
TNC
TNC_CrossCorrFromTimesList.m
TNC
TNC_CrossCorrNormed.m

TNC_QuantCondProb.m
  FUNCTION DETAILS: Function assesses the probability of detecting a given word (MERNUM-mer) prior to a given condition (ACTUAL) in the dataset (DATAARRAY). Significance is assessed by comparing this number of observations to SHUFFNUM random shufflings and resamplings of the data.
  
TNC_QuantISI.m
  FUNCTION DETAILS: Calculate the properties of the interspike interval distribution. Includes: calculation of instantaneous ISI, creation of histograms with linear and log spacing, projection onto a classifier space, calculation of 1st moment properties
  
TNC_QuantMap.m
  FUNCTION DETAILS: analysis of the autocorrelation (peaks, maximal amp, peak fwhm, peak spacing)
  
TNC_QuantPeak.m
  FUNCTION DETAILS: input data must be a vector. From that, parameterized by the threshold, window, and sign of slope this function extracts all peaks that it finds.
  
TNC_QuantRespClass.m
  FUNCTION DETAILS: function implements the presumed method of a class called a 'responseclass'. Idea is that you might derive some classification of responses based upon clustering, trial type, etc. and mean statistics on these subsets can be calculated/extracted for plotting or further analysis.
  
TNC_QuantSegmentedPSTH.m
  FUNCTION DETAILS: function implements the presumed method of a class called a 'responseclass'. Idea is that you might derive some classification of responses based upon clustering, trial type, etc. and mean statistics on these subsets can be calculated/extracted for plotting or further analysis.
  
TNC_QuantSpksPerTrial.m
TNC



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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/SpikeSortLOCAL

TNC_SS_AddCluster.m
TNC
TNC_SS_AddSeeds.m
TNC
TNC_SS_AutoCluster.m
TNC
TNC_SS_CalcClusterEllipse.m
TNC
TNC_SS_CreateSortStruct.m
TNC
TNC_SS_CropCluster.m

TNC_SS_DelCluster.m
TNC
TNC_SS_FindOptimalBoundary.m

TNC_SS_GUI.m
  TNC
TNC_SS_GrowClusterBounds.m
TNC
TNC_SS_LoadClust.m
TNC
TNC_SS_LoadSortedIds.m
TNC
TNC_SS_PropClust.m
TNC
TNC_SS_SaveSortedIds.m
TNC
TNC_SS_StoreClust.m
TNC
TNC_SS_UpdateClusterBoundaries.m
TNC
TNC_SS_UpdateClusterCenters.m
TNC
TNC_SS_UpdateGraphs.m
TNC
TNC_SS_WriteData.m



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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/SpikeSorterGUI

TNC_SS_AddCluster.m
TNC
TNC_SS_AddSeeds.m
TNC
TNC_SS_AutoCluster.m
TNC
TNC_SS_CalcClusterEllipse.m
TNC
TNC_SS_CreateSortStruct.m
TNC
TNC_SS_CropCluster.m

TNC_SS_DelCluster.m
TNC
TNC_SS_FindOptimalBoundary.m

TNC_SS_GUI.m
  TNC
TNC_SS_GrowClusterBounds.m
TNC
TNC_SS_LoadSortedIds.m
TNC
TNC_SS_PropClust.m
TNC
TNC_SS_SaveSortedIds.m
TNC
TNC_SS_StoreAutoClustIds.m
TNC
TNC_SS_UpdateClusterBoundaries.m
TNC
TNC_SS_UpdateClusterCenters.m
TNC
TNC_SS_UpdateGraphs.m
TNC
TNC_SS_WriteData.m

startup.m



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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/StandaloneWrappers

TNC_ExtractMovementWrapper.m
  FUNCTION DETAILS: Wrapper to allow extraction of all movement data from an entire seq file through a series of chunks that are assembled into one data structure.
  
TNC_VideoCompressWrapper.m
TNC


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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/TestScripts

hazardScript.m

plotSandbox.m

swcUtilities.m

testScript.m



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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/TrajectoryAnalysis

TNC_AlignTraj2d.m
TNC
TNC_BatchProcessMoverCSVdata.m

TNC_LeverReport.m

TNC_LoadOpenFieldCheapTracker.m
  PARAMETERS OF ANALYSIS
  Create the filename list from the current directory
  fileDirectory = 'C:\Users\babita\Documents\HHMI\Mitopark\Open Field\MP1\'
  fileDirectory = '/Users/dudmanj/Documents/Work/Janelia/
TNC_MoverBehaviorExtract.m

TNC_NewLeverTrajectoryAnalysis.m
  FUNCTION DETAILS: Analysis of continuous position and velocity data acquired through the MOVER behavior program.
  
TNC_OpenFieldHipp.m

TNC_OpenFieldReport.m

TNC_OpenFieldReportJustTrack.m

TNC_ReachExtract.m
TNC
TNC_ReachVigorWindow.m
TNC
TNC_TransformTrajectory.m
  FUNCTION DETAILS: Utility to transform continuous poisiton trajectories
  into radial distance and heading angles using arbitrary bin sizes to
  compute heading (window) and arbitrary number of angular bins (numBins).
  


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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/Transforms

TNC_ConvertContToEvent.m
  FUNCTION DETAILS: event pulses are obtained from continuous recordings and stored as small structures
  
TNC_ConvertScatterToMatrix.m
  FUNCTION DETAILS: Use an X, Y vector pair of data and convert into an evenly sampled density matrix
  
relu.m



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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/VideoFunctions

TNC_ExtractAndCleanROI.m



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/Users/dudmanj/Dropbox (Personal)/_LAB_Analysis_Scripts/TONIC_v2/Visualization

TNC_AnimatePopVector.m

TNC_CustomRasterPlotter.m
TNC
TNC_DisplayExampleWaveforms.m
TNC
TNC_DisplayShank.m
  FUNCTION DETAILS: Plots data from all electrodes on a given shank to the current axes
      fileNameStr >> name of the ns5 file from which data is loaded
      arrayType >> electrode array type: 'NN
TNC_EvolveContOverTime.m
  FUNCTION DETAILS: function is designed to create a matrix of all recorded electrode channels per time point. the time series of matrices are stored in the cell array "waveRep"
  
TNC_ExtractPopVector.m
TNC
TNC_FormatGraph.m
TNC
TNC_GetMeanData.m
  FUNCTION DETAILS: Calculate the mean data from a passed cellArray containing matrices of repeated observations (rows) of continuous time series data (each time point is a column). The function returns an object that contains the mean data and a user-definable type of positive and negative error vectors.
  
TNC_GetTemplate.m
TNC
TNC_GridCellReport.m
  FUNCTION DETAILS:% simple function meant to generate a report of assorted properties from the spikeMap structure that quantify the properties of the resulting response map.
  
TNC_MoverSessionPlotter.m

TNC_MyPrefSurfPlot.m
TNC
TNC_NormDataMat.m
  FUNCTION DETAILS:
  
TNC_POP_AlignedRaster.m

TNC_POP_AllCrossCorr.m

TNC_POP_DimReduce.m

TNC_PlotContour.m
TNC
TNC_PlotEachCh.m
  FUNCTION DETAILS: Plotting of up to three data segments from each channel of a continuous recording in a single matrix-style plot.
  
TNC_PlotHahnloserRaster.m

TNC_PlotNCTraces.m
TNC
TNC_PlotRaster.m

TNC_RemapElecPos.m
  FUNCTION DETAILS: For a given style of array this function will remap electrode numbers into row and column position on the silicon probe arrray. Together with row spacing and column spacing this can be used to create physical maps of the electrode arrays or associated activity on the arrays
  
TNC_SpkFreqByPosition.m
  FUNCTION DETAILS: 
  
TNC_TrigPopPlotter.m
TNC
TNC_WatchAllChanEvolve.m
  FUNCTION DETAILS: animates a cell array of matrices
  
arrow.m

calculateEllipse.m