The Chronux Package

Chronux is an open-source software package being developed for the analysis of neural data. It is a collaborative research effort based at the Mitra Lab in Cold Spring Harbor Laboratory that has grown out of the work of several groups. Chronux routines may be employed in the analysis of both point process and continuous data, ranging from preprocessing, exploratory and confirmatory analysis.

Chronux offers several routines for computing spectra and coherences for both point and continuous processes. In addition, it also offers several general purpose routines that we have found useful such as a routine for extracting specified segments from data, or binning spike time data with bins of a specified size. Since the data can be continuous valued, point process times, or point processes that are binned, methods that apply to all these data types are given in routines whose names end with 'c' for continuous, 'pb' for binned point processes, and 'pt' for point process times. Thus, mtspectrumc computes the spectrum of continuous data, mtspectrumpb computes a spectrum for binned point processes, and mtspectrumpt compute spectra for data consisting of point process times. Hybrid routines are also available and similarly named - for instance coherencycpb computes the coherency between continuous and binned point process data.

Basic information about common parameters passed to Chronux can be obtained by typing 'help chronux' at the Matlab command prompt (after setting your paths correctly). The expected format for all passed data is explained there, and the ubiquitous 'params' structure for spectral calculations is described in detail. More information can be found in the M2HTML documentation.

The organization of the Main Chronux directory is as follows:

chronux

The main directory for Chronux

chronux/spectral_analysis/continuous

Routines for dealing with continuous or sampled data

chronux/dataio

Routines for reading in NEX, PLX and DDT data files

chronux/spectral_analysis/helper

Various helper routines not usually called directly

chronux/spectral_analysis/hybrid

Routines to compute Coherency and spike triggered averages for mixed format data.

chronux/locfit

The Matlab Locfit package by Catherine Loader

chronux/old

Depecrated routines, kept for backwards compatibility

chronux/spectral_analysis/plots

Assorted plotting commands, with error bars

chronux/spectral_analysis/pointbinned

Routines for dealing with binned point process data

chronux/spectral_analysis/pointtimes

Routines for dealing with point process data stored as times

chronux/spectral_analysis/specscope

Real time multitaper audio spectrogram

chronux/spectral_analysis/statistical_tests

Two group tests for coherence and spectrum

chronux/wave_browser

Experimental GUI-based software for segmenting and classifying audio syllables.

chronux/fly_track

Experimental GUI-based software for fly tracking and analysis.