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

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Accession:225311
"Recorded potentials in the extracellular space (ECS) of the brain is a standard measure of population activity in neural tissue. Computational models that simulate the relationship between the ECS potential and its underlying neurophysiological processes are commonly used in the interpretation of such measurements. Standard methods, such as volume-conductor theory and current-source density theory, assume that diffusion has a negligible effect on the ECS potential, at least in the range of frequencies picked up by most recording systems. This assumption remains to be verified. We here present a hybrid simulation framework that accounts for diffusive effects on the ECS potential. ..."
Reference:
1 . Halnes G, Mäki-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:e1005193 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Extracellular; Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s): Neocortex U1 L6 pyramidal corticalthalamic GLU cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: MATLAB; NEURON;
Model Concept(s): Extracellular Fields;
Implementer(s): Halnes, Geir [geir.halnes at nmbu.no]; Maki-Marttunen, Tuomo [tuomo.maki-marttunen at tut.fi];
Search NeuronDB for information about:  Neocortex U1 L6 pyramidal corticalthalamic GLU cell;
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calcsumcurr_manyareagsynmediumtau_parts_fixeddt.py
combinemattomat_fixeddt.m
interpolate.m *
interpolate_multidim.m *
summondata.m
sumrepetitions_seed.m
                            
% combinemattomat_fixeddt.m
% A MATLAB script for combining the files saved by running "calcsumcurr_manyareagsynmediumtau_parts_fixeddt.py 20 0.025 0.000042 10000 10000 2 myseed 200"
% Expects that the variable "myseed" has been initialized
% Tuomo Maki-Marttunen, 2014-2016

synloctype = 2;
nsegs = 20;
dt = 0.025;
tstop = 10000;
Nsynlocs = 10000;
singleSimT = 200;

syngmaxes = [nan 0.000042 nan];
syngmax = syngmaxes(synloctype);

Nsims = floor(1.0*tstop/singleSimT+0.9999);
Nparts = 13;
ina = [];
ik = [];
ica = [];
ih = [];
il = [];
VtimesA = [];
imemb = [];
Vsoma = [];
icap = [];
times = [];
dt_int = 0.1;

tic
for isim=1:Nsims
  disp(['isim=' num2str(isim)]);
  disp(['Loading isim=' num2str(isim) ', myseed=' num2str(myseed) ', toc=' num2str(toc)]);
  A = load(['currsums_parts_' num2str(Nsynlocs) 'areagsynsmediumtau_fixeddt_type' num2str(synloctype) '_amp' num2str(syngmax) '_tstop' num2str(tstop) '.0_nseg' num2str(nsegs) '_dt' num2str(dt) '_seed' num2str(myseed) '_sim' num2str(isim-1) 'x200.0.mat']);

  times = [times;A.times];
  ina = [ina, A.ina];
  ik = [ik, A.ik];
  ica = [ica, A.ica];
  ih = [ih, A.ih];
  il = [il, A.il];
  VtimesA = [VtimesA, A.VtimesA];
  imemb = [imemb, A.imemb];
  icap = [icap, A.icap];
  Vsoma = [Vsoma; A.Vsoma];

  if isim==1
    ts_syn = A.ts_syn;
    part_syn = A.part_syn;
  end
end

clear A
clear isim
clear Nsims
clear dt_int
clear ts


save(['currsums_parts_' num2str(Nsynlocs) 'areagsynsmediumtau_fixeddt_type' num2str(synloctype) '_amp' num2str(syngmax) '_tstop' num2str(tstop) '.0_nseg' num2str(nsegs) '_dt' num2str(dt) '_seed' num2str(myseed) '_comb200.0.mat']);

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