Chronux is an open-source software package developed for the loading, visualization and analysis of a variety of modalities / formats of

neurobiological Neuroscience is the scientific study of the nervous system (the brain, spinal cord, and peripheral nervous system), its functions and disorders. It is a multidisciplinary science that combines physiology, anatomy, molecular biology, developme ...

time series In mathematics, a time series is a series of data points indexed (or listed or graphed) in time order. Most commonly, a time series is a sequence taken at successive equally spaced points in time. Thus it is a sequence of discrete-time data. Ex ...

data. Usage of this tool enables

neuroscientist A neuroscientist (or neurobiologist) is a scientist who has specialised knowledge in neuroscience, a branch of biology that deals with the physiology, biochemistry, psychology, anatomy and molecular biology of neurons, neural circuits, and glial ...

s to perform a variety of analysis on multichannel electrophysiological data such as LFP (local field potentials),

EEG Electroencephalography (EEG) is a method to record an electrogram of the spontaneous electrical activity of the brain. The biosignals detected by EEG have been shown to represent the postsynaptic potentials of pyramidal neurons in the neocortex ...

, MEG, Neuronal spike times and also on spatiotemporal data such as

FMRI Functional magnetic resonance imaging or functional MRI (fMRI) measures brain activity by detecting changes associated with blood flow. This technique relies on the fact that cerebral blood flow and neuronal activation are coupled. When an area ...

and dynamic optical imaging data. The software consists of a set of

MATLAB MATLAB (an abbreviation of "MATrix LABoratory") is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks. MATLAB allows matrix manipulations, plotting of functions and data, implementa ...

routines interfaced with C libraries that can be used to perform the tasks that constitute a typical study of neurobiological data. These include

local regression Local regression or local polynomial regression, also known as moving regression, is a generalization of the moving average and polynomial regression. Its most common methods, initially developed for scatterplot smoothing, are LOESS (locally e ...

and

smoothing In statistics and image processing, to smooth a data set is to create an approximating function that attempts to capture important patterns in the data, while leaving out noise or other fine-scale structures/rapid phenomena. In smoothing, the dat ...

, spike sorting and spectral analysis - including multitaper spectral analysis, a powerful

nonparametric Nonparametric statistics is the branch of statistics that is not based solely on Statistical parameter, parametrized families of probability distributions (common examples of parameters are the mean and variance). Nonparametric statistics is based ...

method to estimate power spectrum. The package also includes some GUIs for time series visualization and analysis. Chronux is GNU GPL v2 licensedhttp://chronux.org/downloads/chronux/chronux/manual.pdf (and MATLAB is proprietary). The most recent version of Chronux is version 2.12.

History

From 1996 to 2001, the

Marine Biological Laboratory The Marine Biological Laboratory (MBL) is an international center for research and education in biological and environmental science. Founded in Woods Hole, Massachusetts, in 1888, the MBL is a private, nonprofit institution that was independent ...

(MBL) at Woods Hole, Massachusetts, USA hosted a workshop on the analysis of neural data. This workshop then evolved into the special topics course on

neuroinformatics Neuroinformatics is the field that combines informatics and neuroscience. Neuroinformatics is related with neuroscience data and information processing by artificial neural networks. There are three main directions where neuroinformatics has to be ...

which is held at the MBL in the last two weeks of August every year. The popularity of these pedagogical efforts and the need for wider dissemination of sophisticated

time-series analysis In mathematics, a time series is a series of data points indexed (or listed or graphed) in time order. Most commonly, a time series is a sequence taken at successive equally spaced points in time. Thus it is a sequence of discrete-time data. Ex ...

tools in the wider

neuroscience Neuroscience is the scientific study of the nervous system (the brain, spinal cord, and peripheral nervous system), its functions and disorders. It is a multidisciplinary science that combines physiology, anatomy, molecular biology, developme ...

community led the Mitra Lab at Cold Spring Harbor Laboratory to initiate an NIH funded effort to develop software tools for neural data analysis in the form of the Chronux package. Chronux is the result of efforts of a number of people, the chief among whom are Hemant Bokil, Peter Andrews, Samar Mehta, Ken Harris, Catherine Loader, Partha Mitra, Hiren Maniar, Ravi Shukla, Ramesh Yadav, Hariharan Nalatore and Sumanjit Kaur. Important contributions were also made by Murray Jarvis, Bijan Pesaran and S.Gopinath. Chronux welcome contributions from interested individuals.

Organization and capabilities of Chronux

Chronux is organized into a number of distinct toolboxes. These include the spectral analysis toolbox, the

and

likelihood The likelihood function (often simply called the likelihood) represents the probability of random variable realizations conditional on particular values of the statistical parameters. Thus, when evaluated on a given sample, the likelihood functi ...

toolbox, and the spike-sorting toolbox. In addition, a number of domain-specific GUIs are part of the Chronux package and more are envisaged. Much of Chronux is written in

with certain intensive computations being coded in C with a MEX interface to MATLAB. The methods employed are state-of-the-art: For example, the spectral analysis toolbox implements the multitaper spectral estimation method and the local regression and Likelihood toolbox (Locfit) implements a set of highly flexible methods for fitting functions and

probability distributions In probability theory and statistics, a probability distribution is the mathematical function that gives the probabilities of occurrence of different possible outcomes for an experiment. It is a mathematical description of a random phenomenon ...

to data. Chronux provides robust estimates of the confidence intervals on computed quantities. Thus, the computation of a spectrum can be augmented by a computation of both asymptotic and jackknife based

confidence intervals In frequentist statistics, a confidence interval (CI) is a range of estimates for an unknown parameter. A confidence interval is computed at a designated ''confidence level''; the 95% confidence level is most common, but other levels, such as 9 ...

and the same is true of most quantities in the spectral analysis toolbox. Similarly, the local regression and likelihood toolbox is a MEX front-end to the Locfit package which provides a comprehensive set of tools for model testing and validation.

The graphical user interface

The GUI can be invoked from the MATLAB prompt by typing ndb – short for the Neuro Data Browser (NDB) – which provides a standard user interface for loading, visualizing and analyzing neurobiological time series data. The data can be in different formats such as EEG, MEG, FMRI etc. A standard UI for selecting and visualizing relevant portions (samples/channels/trials) of the time series is used so that it is possible to view, store and analyze the data for a typical study – which can be of the order of several Gb's – from multiple modalities / formats on a single platform. The GUI also provides the facility to view a summary of all the data objects that have been added to the system pool. Currently there are two views of the summarized data – by patient name and by modality/format. At a basic level, the GUI enables users, to load data, analyze them and visualize the results within the Browser framework without a need to write separate MATLAB codes. For advanced users, it also provides a

command line A command-line interpreter or command-line processor uses a command-line interface (CLI) to receive commands from a user in the form of lines of text. This provides a means of setting parameters for the environment, invoking executables and pro ...

interface, so that data can be directly loaded and visualized for analysis. The usage of

XML Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable ...

based plugin-architecture allows for extending support to other modalities and formats and also serves to integrate any other MATLAB toolbox with minimal changes in the plugin XML. The M2HTML documentation is an archive of online help for all MATLAB routines incorporated in Chronux. This consists of function descriptions and dependency graphs.

References

{{reflist *Partha Mitra and B. Pesaran, "Analysis of Dynamic Brain Imaging Data." The Biophysical Journal, Volume 76 (1999), 691–708
arxiv.org/abs/q-bio/0309028
*Partha Mitra and Hemant Bokil. ''Observed Brain Dynamics'', Oxford University Press, USA (2007)
Link connecting the Book
*Donald. B. Percival and Andrew. T. Walden. ''Spectral Analysis for Physical Applications: Multitaper and Conventional Univariate Techniques'', Cambridge University Press, UK (2002). *Peter Stoica and Randolph. L. Moses. ''Introduction to Spectral Analysis'', Prentice Hall, USA (1997). *Richard Shiavi. ''Introduction to Applied Statistical Signal Analysis'', Academic Press, (1999).

External links

Welcome to Chronux
Free mathematics software Signal processing