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Transfer Entropy Software of paper "Shifts of Gamma Phase across Primary Visual Cortical Sites Reflect Dynamic Stimulus-Modulated Information Transfer" published by Besserve et al in Plos Biology 2015 Transfer Entropy Software of paper "Shifts of Gamma Phase across Primary Visual Cortical Sites Reflect Dynamic Stimulus-Modulated Information Transfer" published by Besserve et al in Plos Biology 2015

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Date added: 09/21/2015
Date modified: 10/08/2015
Filesize: Unknown
Downloads: 586
The data that underlie the main text and supplementary figures of this paper, as well as the code for the transfer entropy calculation, can be found at http://dx.doi.org/10.6084/m9.figshare.1460872

State-discounted information calculation software State-discounted information calculation software

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Date added: 09/28/2015
Date modified: 10/12/2015
Filesize: 6 kB
Downloads: 869
This software computes mutual information between stimuli and neural response both after discounting the state variability and without considering the state variability. This software also provides a simulation of Poisson neurons that responds to stimuli and that has an additive state dependent component. This simulation may be useful to users to try out the software and test some ideas. These methods developed and used in papers:

 H. Safaai, R. Neves, O. Eschenko, N. K. Logothetis, Stefano Panzeri, A dynamical model of  the effect of Locus Coeruleus firing on single-trial cortical state dynamics and sensory, PNAS 2015, ; published ahead of print September 28, 2015, doi:10.1073/pnas.1516539112

C. Kayser, C. Wilson, H. Safaai, S. Sakata, S. Panzeri, Rhythmic Auditory Cortex Activity at Multiple Timescales Shapes Stimulus–Response Gain and Background FiringThe Journal of Neuroscience,35(20): 7750-7762; doi: 10.1523/JNEUROSCI.0268-15.2015

Any person downloading this software accepts to acknowledge this study by citing it in every publication or report arising from the use of this material. 

The folder contains the following set of functions to compute the information of the discounted trial-to-trial variability.

STATE_INFORMATION.m: The function computes the following three information values

Information between the stimulus and response I(S,R)

Information between the stimulus and discounted variability response I(S;R’) where the trial-to-trial variability V is subtracted from the response as R’=R-V.

The joint information between the stimulus and the response and state I(S;R,theta)

State_Variability_Simulator.m: The functions simulates responses of a poisson process with the trial-to-trial variability which is a linearly related to the phase of the ongoing activity at the moment of stimulus onset. The function first simulates the data, then estimates the trial-to-trial variability by fitting the data to the linearly additive state model and then apply the fit to a cross-validated test set. This function uses the functions lint.m and fit_lintr.m functions to fit the linear additive state model to the data.

Main.m: This is the main file which can be used to either simulate the trial-to-trial variability or use the DATA.mat file as the input of the STATE_INFORMATION.m function. The output will be a bar plot of different information values.

Software of simulation of current based and conductance based integrate and fire network Software of simulation of current based and conductance based integrate and fire network

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Date added: 10/08/2015
Date modified: 10/08/2015
Filesize: Unknown
Downloads: 648
Here we report the code developed and used in the paper:

Cavallari S, Panzeri S and Mazzoni A (2014) Comparison of the dynamics of neural interactions between current-based and conductance-based integrate-and-fire recurrent networks. Front. Neural Circuits 8:12. doi: 10.3389/fncir.2014.00012

The code is made available in the ModelDB sharing repository:
http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=152539

with accession number 152539



Software for space-by-time non-negative matrix factorization Software for space-by-time non-negative matrix factorization

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Date added: 10/08/2015
Date modified: 10/08/2015
Filesize: Unknown
Downloads: 664
Here we show the link to the software for space-by-time separable non-negative matrix factorization that was developed by Delis and colleagues and published in the following article:

Delis I., Panzeri S., Pozzo T., Berret B. (2014) A unifying model of concurrent spatial and temporal modularity in muscle activity, J Neurophysiol 111: 675–693

This software can be found at:
http://hebergement.u-psud.fr/berret/software/sNM3F.zip

Software for non-stationary time-dependent analysis of spike trains based on wavelets (Dos Santos et al) Software for non-stationary time-dependent analysis of spike trains based on wavelets (Dos Santos et al)

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Date added: 02/27/2015
Date modified: 02/27/2015
Filesize: Unknown
Downloads: 861

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FP7-70pxeu-flag-70pxfet-70pxThe project SI-CODE acknowledges the financial support of the Future and Emerging Technologies (FET) programme within the Seventh Framework Programme for Research of the European Commission, under FET-Open grant number: FP7-284553