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Number of citations per year for the bioinformatics software tool Chronux

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Chronux specifications


Unique identifier OMICS_28504
Name Chronux
Software type Toolkit/Suite
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, MATLAB
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.12
Stability Stable
Maintained Yes




No version available



  • person_outline Peter Andrews
  • person_outline Hemant Bokil

Publication for Chronux

Chronux citations


Circadian and Brain State Modulation of Network Hyperexcitability in Alzheimer’s Disease

PMCID: 5956746
PMID: 29780880
DOI: 10.1523/ENEURO.0426-17.2018

[…] and dividing by the total number of hours the patient spent in each respective sleep stage in the recording.Spectral analysis of the FO electrodes was performed in MATLAB, using the freely available Chronux toolbox (). Analysis was performed on the LFO1, LFO2, RFO1, and RFO2 channels, as these were the deepest contacts and thus least prone to noise or artifact. Channels were each normalized to ze […]


Olfactory inputs modulate respiration related rhythmic activity in the prefrontal cortex and freezing behavior

Nat Commun
PMCID: 5906445
PMID: 29670106
DOI: 10.1038/s41467-018-03988-1
call_split See protocol

[…] Acquired data were processed offline using custom Matlab scripts and the multitaper spectral methods included in the Chronux toolbox. Differential LFPs were calculated as the difference between pairs of neighboring electrodes in the same brain area to achieve spatially local measurements of electrical activities and […]


Differences in the Electrophysiological Properties of Mouse Somatosensory Layer 2/3 Neurons In Vivo and Slice Stem from Intrinsic Sources Rather than a Network Generated High Conductance State

PMCID: 5898699
PMID: 29662946
DOI: 10.1523/ENEURO.0447-17.2018

[…] frequency value associated with f-I curves. For slice and in vivo comparisons in pyramidal cells, we used a 0.5-long pulse.For power spectral density curves and spectrogram analyses (, ), we used the Chronux ( analysis software toolkit developed in MATLAB (Mathworks). For spectrograms, mean-subtracted, 2-min-long voltages traces were low-pass filtered at 1000 Hz and then analyz […]


Long wavelength (reddish) hues induce unusually large gamma oscillations in the primate primary visual cortex

Proc Natl Acad Sci U S A
PMCID: 5924890
PMID: 29632187
DOI: 10.1073/pnas.1717334115

[…] session owing to pseudorandom stimulus presentation and removal of some repeats from analyses after artifact rejection). Spectral analyses were done using the Multitaper method using functions in the Chronux toolbox () ( developed for MATLAB. Time-frequency power spectra were obtained with a single taper with a sliding window of 0.25 s to obtain a 4-Hz frequency resolution. Power spec […]


Theta Oscillations Organize Spiking Activity in Higher Order Visual Thalamus during Sustained Attention

PMCID: 5881415
PMID: 29619407
DOI: 10.1523/ENEURO.0384-17.2018

[…] pulvinar spikes and the LFP at different epochs during the task, we computed the spike-field coherence (SFC) of simultaneously recorded spike trains and LFP using multi-taper analysis provided by the Chronux data analysis toolbox (). The SFC was calculated in 2 s windows using the coherencycpt function for each epoch (before initiation, before stimulus onset, before screen touch and after screen t […]


Closed Loop Deep Brain Stimulation for Refractory Chronic Pain

Front Comput Neurosci
PMCID: 5879131
PMID: 29632482
DOI: 10.3389/fncom.2018.00018

[…] cy representation of the raw LFP signal, we use a variant of the discrete Fourier Transform (DFT). There are multiple methods to implement a DFT- we prefer using the multitaper DFT implemented in the Chronux Toolbox for MATLAB, which reduces broadband bias (Bokil et al., ). To adequately sample pain states, we propose to use at-home, patient-triggered recordings be collected. Two data collection s […]

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Chronux institution(s)
Medametrics, LLC, New York, NY, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; School of Medicine, SUNY Downstate Medical Center, New York, NY, USA
Chronux funding source(s)
Supported by grant R01MH071744 from NIH.

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