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Effect of ionic diffusion on extracellular potentials (Halnes et al 2016)

modeldb.science/225311

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Name		Name	Last commit message	Last commit date
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haymod_sumcurr		haymod_sumcurr
Nfreq5.m		Nfreq5.m
PLoSdataplot.m		PLoSdataplot.m
PLoSdynplot.m		PLoSdynplot.m
PLoSfreqplot.m		PLoSfreqplot.m
PLoSsilenceplot.m		PLoSsilenceplot.m
PLoStempplot.m		PLoStempplot.m
mosinit_n_rev.m		mosinit_n_rev.m
nvoxels.m		nvoxels.m
readme.html		readme.html
runit.m		runit.m
screenshot1.png		screenshot1.png
screenshot2.png		screenshot2.png
screenshot3.png		screenshot3.png
screenshot4.png		screenshot4.png
screenshot5.png		screenshot5.png
screenshot6.png		screenshot6.png
screenshot7.png		screenshot7.png
screenshot8.png		screenshot8.png

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Matlab files for the article: 

Halnes G, Maki-Marttunen T, Keller D, Pettersen KH, Andreassen OA,
Einevoll GT (2016). Effect of Ionic Diffusion on Extracellular
Potentials in Neural Tissue. PLoS Comput Biol 12(11): e1005193
<a href="http://dx.doi.org/10.1371/journal.pcbi.1005193">http://dx.doi.org/10.1371/journal.pcbi.1005193</a>

This archive was contributed by G Halnes.

The article presents a modelling study performed in two steps. First,
the NEURON-simulator was used to compute the output time series of a
population of ten pyramidal neurons. Next, this output was used as
"input" to a MATLAB-simulation of the extracellular dynamics of the
electrical potential and ion concentrations (K+, Na+, Ca++ and an
unspesified negative ion X-) surrounding the population of neurons.

The MATLAB code:

mosinit_n_rev.m runs the extracellular simulation for a given neuronal
output time series. In order for mosinit_n_rev to run, the data file
revdata.mat must be found in the same folder. The file revdata.mat is
made available for users from the below link:

<a href="https://senselab.med.yale.edu/ModelDB/data/225311/revdata.mat">https://senselab.med.yale.edu/ModelDB/data/225311/revdata.mat</a>

so that the extracellular simulations (MATLAB code) can be run without
re-running the simulations of neuronal output (NEURON code).

mosinit_n_rev.m runs three simulations, each covering 84 s of
biological time. The results are saved in the files (1)
'Sim_diffon.mat', (2) 'Sim_diffoff.mat' and (3) 'Sim_dead.mat'. These
files contain all simulation data, and are called by mosinit_n_rev
when results are plotted. These simulations represent cases with (1)
diffusion present in the extracellular space, (2) diffusion not
present in the extracellular space, and (3) diffusion present, but
neurons turned off halfway in the simulation, i.e., after 42 s. The
total simulation time (i.e. the time to run all three simulations)
should be about 1-3 hours on a regular laptop (3 hours on a 2011
laptop).

Eight figures from the paper are generated by mosinit_n_rev.m:

Figure 2:
<img src="./screenshot1.png" alt="screenshot 1" width="550">

Figure 3:
<img src="./screenshot2.png" alt="screenshot 2" width="550">

Figure 4:
<img src="./screenshot6.png" alt="screenshot " width="550">

Figure 5:
<img src="./screenshot3.png" alt="screenshot " width="550">

Figure 6:
<img src="./screenshot4.png" alt="screenshot " width="550">

Figure 7:
<img src="./screenshot5.png" alt="screenshot " width="550">

Figure 8:
<img src="./screenshot7.png" alt="screenshot " width="550">

Figure 9:
<img src="./screenshot8.png" alt="screenshot " width="550">

The NEURON code:

For users who want to compute the neuron output data, the NEURON-code
used to generate revdata.mat is made available for users. To run this
(and generate the revdata.mat file), use the NEURON-code and
instructions found in the folder haymod_sumcurr.
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