Chronux

Chronux Analysis Software

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

The current release of Chronux is implemented as a Matlab library. The release notes can be found here. There is a test data suit for this release, which can be downloaded by clicking here.

Chronux Tutorials

These tutorials can help you to get started using Chronux.

These tutorials are part of the chronux distribution, and were created for the 2006 SfN Dynamical Neuroscience workshop. The Matlab scripts are meant to be run while viewing the presentations. You must first install Chronux to use most of the tutorials.

Tutorials:

• Partha Mitra: PDF Talk.
• Bijan Pesaran: PowerPoint Talk.
• Hemant Bokil: Whole tutorial (Powerpoint) or just the Powerpoint Talk.
• Keith Purpura: Whole tutorial (Powerpoint) or just the Powerpoint Talk.
• Chris Fall: Whole tutorial (Powerpoint) or just the Powerpoint Talk.

Chronux Documentation

The Chronux Manual describes how to use Chronux.

M2HTML generated documentation can be found here.

Chronux News

• Chronux version 2.12 was released April 20, 2016. This release has an optimized version of the mtspecgrampt.m function, called mtspecgrampt_optimized.m.

• Chronux version 2.11 was released October 01, 2012. This release has fixes to several reported bugs.

• Chronux version 2.10 was released August 12, 2011. Significant changes are: Various bugs have been fixed in this release.

  The following routines have been modified since the version 2.00 release: findpeaks, coherr, mtspecgramc, coherencyc, two_group_test_spectrum, two_group_test_coherence, mtspectrumc_unequal_length_trials, CrossSpecMatc, CrossSpecMatpt, CrossSpecMatpb, mtspecgrampt, mtspecgrampb, nonst_stat, and quadcof.

  The spike-sorting subpackage is no longer included in the Chronux package. An updated spike-sorting package may now be found at Dr. Kleinfeld's Lab website: http://physics.ucsd.edu/neurophysics/links.html.

• Chronux version 2.00 was released August 16, 2008. Significant changes are: Added Ftrack fly tracking subpackage, updated locfit version with self-describing output format, spectral analysis routines added for unequal length trials, assorted bugfixes, and manual added.

• 2012 was the the eleventh year of the Neuroinformatics summer course at the Marine Biological Laboratory, Woods Hole.