Viewer for electrophysiological and behavioral data

NeuroScope

Developed by Lynn Hazan (User manual written by Lynn Hazan and Michael B. Zugaro )

The initial seeds of this software were created by Jozsef Csicsvari

NeuroScope can display local field potentials (EEG), neuronal spikes, behavioral events, as well as the position of the animal in the environment. It also features limited editing capabilities.

Software for Manual Clustering

Klusters

Developed by Lynn Hazan (User manual written by Michael B. Zugaro )

The initial seeds of this software were created by Jozsef Csicsvari

Klusters is a powerful and easy-to-use cluster cutting application designed to help neurophysiologists sort action potentials from multiple neurons on groups of electrodes (e.g., tetrodes or multisite silicon probes).

 Software for Automatic Clustering

Developed by Kenneth D. Harris

KlustaKwik is a program for automatic cluster analysis, specifically designed to run fast on large data sets.

Download the latest linux version HERE (versions below may not be up to date)
Download Windows executable HERE (Compiled by Samar Mehta )
Download MacOS X package HERE (Compiled by Peter Steinmetz)

MATLAB m-files

A selection of MATLAB files developed in the lab can be found here. Feedback is appreciated.

Toolbox contents

CanonCor - cannonical correlation analysis
CanonCor2 - predictive cannonical correlation analysis
ColoredNoise - generates gaussian noise with required power spectrum
Comodugram - looks for comodulations in power spectra of a multiple time series (with correlation coefficient)
Comodugram2 - does the same thing in a differnent way (with E(XY) / (E(X)*E(Y))
Comoherogram - looks for comodulations in power spectra and coherences of a multiple time series
ComplexImage - plots a pseudocolor plot of a complex matrix where brightness is amplitude and hue is phase
Clustogram - Draws a shaded clustogram from the Feature file and cluster file.
ColorScatter -draws a 2d scatter plot of the data with colors allocated according to the vector Colors
CrossTab - cross-tabulates co-occurences of unique values in two lists
CrossTabPlot - Graphical test of independence in a cross-table
Csd2Coherence - Converts a cross-spectral matrix to a coherence matrix
CsdCanon - does cannonical coherence analysis, given a cross-spectral matrix
CsdEig - calculates and plots eigenvectors of a cross-spectral matrix
Discrim - linear discriminant analysis
EmpiricalCdf - cumulative distribution function of input data
FileExists - tests if a file exists
FileLength - length of file in bytes
FindEvents - finds spectrally outlying events in a time series
ForAllSubplots - executes a command for every subplot in a figure
ForAllFigures - executes a command for every figure
Harmonix - detects coherent harmonics in a time series
ImageMatrix - plots a matrix of color images from a 4D array
LoadHeadedArray - loads up a file whose first line is column headings
LoadStringArray - Loads a 2d array of strings from a text file
LoadStringList - Loads a 1d array of strings from a text file
LocalMinima -  Finds positions of all strict local minima in input array
MeanSmooth - smooths data with a local mean
MeanSmooth2 - smooths 2d data with a local mean
MedianSmooth - smooths data with a local median
MedianSmooth2 - smooths 2d data with a local median
MultiCohere - takes a multivariate time series and does a matrix of coherence plots
MultiReg - does lots of linear regressions at the same time, so you can regress an entire waveform onto a single variable
NormVector - Takes a matrix that consists of column vectors and normalized each one.
OutlierRemoveAuto - An automatic, iterative function to remove outliers from multivariate data
OutlierRemoveManual - An interactive, iterative function to remove outliers from multivariate data
PlotConic -Plots the conic section that is the solution of x'*M*x + v'*x + c = 0
PlotLine - Plots a line w'*x + b = 0
Quantile - Computes quantile for a single data point relative to a distribution
QuickRegress - quick linear regression plot
PlotMatrix - plots a matrix of line graphs from a 3d array
RandomSample - produces a vector of m integers in the range 1:n without replacement
RealignToPeaks - Realigns waveforms on their peaks
ScaleBar - draws scale bars on a plot
SpikePower - computes the spectra of a set of traces
SpikePowerMTM - computes the spectra of a set of traces using the multitaper method
ThresholdCrossings - finds times when a waveform crosses up through a given threshold
TriggeredAv - computes triggered averages from a trace
WithinRanges - checks which elements of a vector lie in a specified set of ranges
WordCount - counts number of words in a file
bload - loads a binary file
bsave - saves a binary file
chi2plot - displays a Chi^2 plot (to check if data come from a Chi^2 distribution)
clip - limits data above and below
corrcoef2 - correclation matrix for two multivariate data sets
hist2 - plots a 2d histogram
letterlayout - sets the current figure in portlait (US letter size) mode
letterlayoutl - sets the current figure in landscape (US letter size) mode
msave - save a matrix in ascii format
msline - Add a median smooth line to a scatter plot (like lsline)
mtchd - Multi-taper coherence density
mtchg - Multi-taper time-frequency coherence-gram
mtchgnorm - Multi-taper time-frequency coherence-gram, with normalizing transformation
mtcsg - Multi-taper time-frequency cross-spectro-gram
mtcsd - Multi-taper cross-spectrum matrix
mtpsg - Multi-taper time-frequency power spectrogram (i.e. cross-spectra)
pplot - plots graphs one at a time with a pause between
sq - alias for squeeze
xgobi - launches an xgobi session (multivariate visualization)
xgvis - launches an xgvis session (multidimensional scaling)
zTrans - Fisher's z-transform.
 
Further Information

For more information contact Ken Harris