Chronux

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Chronux is an open-source software package developed for the loading, visualization and analysis of a variety of modalities / formats of neurobiological time series data. Usage of this tool enables neuroscientists to perform a variety of analysis on multichannel electrophysiological data such as LFP (local field potentials), EEG, MEG, Neuronal spike times and also on spatiotemporal data such as FMRI and dynamic optical imaging data. The software consists of a set of MATLAB 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 and smoothing, spike sorting and spectral analysis - including multitaper spectral analysis, a powerful nonparametric method to estimate power spectrum. The package also includes some GUIs for time series visualization and analysis. Chronux is GNU GPL v2 licensed [1] (and MATLAB is proprietary).

Time series Sequence of data over time

A time series is a series of data points indexed 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. Examples of time series are heights of ocean tides, counts of sunspots, and the daily closing value of the Dow Jones Industrial Average.

Neuroscientist individual who studies neuroscience

A neuroscientist is a scientist who has specialised knowledge in the field of neuroscience, the branch of biology that deals with the physiology, biochemistry, anatomy and molecular biology of neurons and neural circuits and especially their association with behaviour and learning.

MATLAB multi-paradigm numerical computing environment

MATLAB is a multi-paradigm numerical computing environment and proprietary programming language developed by MathWorks. MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, C#, Java, Fortran and Python.

Contents

The most recent version of Chronux is version 2.12.

History

From 1996 to 2001, the Marine Biological Laboratory (MBL) at Woods Hole, Massachusetts, USA hosted a workshop on the analysis of neural data.[ citation needed ] This workshop then evolved into the special topics course on neuroinformatics 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 tools in the wider neuroscience 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.[ citation needed ] 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.

Marine Biological Laboratory international center for research and education in biology, biomedicine and ecology

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 affiliated with the University of Chicago. After being independent for most of its history, it became affiliated with the university on July 1, 2013. It also collaborates with numerous other institutions.

Neuroinformatics is a research field concerned with the organization of neuroscience data by the application of computational models and analytical tools. These areas of research are important for the integration and analysis of increasingly large-volume, high-dimensional, and fine-grain experimental data. Neuroinformaticians provide computational tools, mathematical models, and create interoperable databases for clinicians and research scientists. Neuroscience is a heterogeneous field, consisting of many and various sub-disciplines. In order for our understanding of the brain to continue to deepen, it is necessary that these sub-disciplines are able to share data and findings in a meaningful way; Neuroinformaticians facilitate this.

Organization and capabilities of Chronux

Chronux is organized into a number of distinct toolboxes. These include the spectral analysis toolbox, the local regression and likelihood 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 MATLAB with certain intensive computations being coded in C with a MEX interface to MATLAB. The methods employed are state-of-the-art[ citation needed ]: 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 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 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.

Local regression

Local regression or local polynomial regression, also known as moving regression, is a generalization of moving average and polynomial regression. Its most common methods, initially developed for scatterplot smoothing, are LOESS and LOWESS, both pronounced. They are two strongly related non-parametric regression methods that combine multiple regression models in a k-nearest-neighbor-based meta-model.

Multitaper

In signal processing, the multitaper method is a technique developed by David J. Thomson to estimate the power spectrum SX of a stationary ergodic finite-variance random process X, given a finite contiguous realization of X as data. It is one of a number of approaches to spectral density estimation.

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

XML Markup language developed by the W3C for encoding of data

Extensible Markup Language (XML) is a markup language that defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. The W3C's XML 1.0 Specification and several other related specifications—all of them free open standards—define XML.

Plug-in (computing) software component that adds a specific feature to an existing software application

In computing, a plug-in is a software component that adds a specific feature to an existing computer program. When a program supports plug-ins, it enables customization.

The M2HTML documentation is an archive of online help for all MATLAB routines incorporated in Chronux. This consists of function descriptions and dependency graphs.

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References

  1. ↑ http://chronux.org/downloads/chronux/chronux/manual.pdf
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