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More parameter tuning 

Signed-off-by: Schellenberger <schellenberger@inb.uni-luebeck.de>
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1 parent 9705fb9 commit 3495bacb8fc43e93fa923974221ec9cca5570281 @miscco committed Oct 31, 2014
Unified Split
Showing with 75 additions and 67 deletions.
  1. +54 −51 Plots.m
  2. +8 −3 Thalamic_Column.cpp
  3. +13 −13 Thalamic_Column.h
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105 Plots.m
@@ -1,82 +1,85 @@
% mex command is given by:
% mex CXXFLAGS="\$CXXFLAGS -std=c++11" TC.cpp Cortical_Column.cpp Thalamic_Column.cpp
-function Plots(T)
-
+function Plots(type)
if nargin == 0
+ type = 1;
+end
+
+if type == 1
- Param_Cortex_N2 = [4.7; % sigma_e
- 1.43; % g_KNa
+ Param_Cortex = [4.7; % sigma_e
+ 1.33; % g_KNa
120E-3]; % dphi
-
- Param_Cortex_N3 = [6.3; % sigma_e
- 2.; % g_KNa
- 120E-3]; % dphi
-
-
- Param_Thalamus_N2 = [0.025; % g_LK_t
- 0.025; % g_LK_r
- 0.08]; % g_h
-
+
+ Param_Thalamus = [0.048; % g_h
+ 0.0245; % g_LK_t
+ 0.0245]; % g_LK_r
+
+else
+ Param_Cortex = [6.05; % sigma_e
+ 2.1; % g_KNa
+ 120E-3]; % dphi
+
+ Param_Thalamus = [0.052; % g_h
+ 0.02; % g_LK_t
+ 0.02]; % g_LK_r
+end
- Param_Thalamus_N3 = [0.021; % g_LK_t
- 0.021; % g_LK_r
- 0.08]; % g_h
-
- Connectivity = [2.4; % N_et
- 2.6; % N_er
- 5; % N_te
- 10]; % N_ti
+Connectivity = [ 3; % N_et
+ 3; % N_er
+ 5; % N_te
+ 10]; % N_ti
- % stimulation parameters
- % first number is the mode of stimulation
- % 0 == none
- % 1 == semi-periodic
- % 2 == phase dependend
+% stimulation parameters
+% first number is the mode of stimulation
+% 0 == none
+% 1 == semi-periodic
+% 2 == phase dependend
- var_stim = [ 2; % mode of stimulation
- 25; % strength of the stimulus in Hz (spikes per second)
- 120; % duration of the stimulus in ms
- 5; % time between stimulation events in s (ISI)
- 0; % range of ISI in s [ISI-range,ISI+range]
- 2; % Number of stimuli per event
- 950; % time between stimuli within a event in ms
- 500]; % time until stimuli after minimum in ms
+var_stim = [ 0; % mode of stimulation
+ 50; % strength of the stimulus in Hz (spikes per second)
+ 120; % duration of the stimulus in ms
+ 5; % time between stimulation events in s (ISI)
+ 0; % range of ISI in s [ISI-range,ISI+range]
+ 1; % Number of stimuli per event
+ 950; % time between stimuli within a event in ms
+ 5]; % time until stimuli after minimum in ms
- T = 30; % duration of the simulation
-end
+T = 30; % duration of the simulation
-[Ve, Vt, Marker_Stim] = TC(T, Param_Cortex_N2, Param_Thalamus_N2, Connectivity, var_stim);
-%[Ve, Vt, Marker_Stim] = TC(T, Param_Cortex_N3, Param_Thalamus_N3, Connectivity, var_stim);
+[Ve, Vt, Marker_Stim] = TC(T, Param_Cortex, Param_Thalamus, Connectivity, var_stim);
-L = max(size(Vt));
+L = length(Vt);
timeaxis = linspace(0,T,L);
figure(1)
subplot(211), plot(timeaxis,Ve)
-title('Pyramidal membrane voltage'), xlabel('time in s'), ylabel('Ve in mV')
+title('Pyramidal membrane voltage'),
+xlabel('Time in s'),
+ylabel('V_{e} in mV')
ylim([-80, -40])
% vertical line for markers
for i=1:var_stim(6)
hx = graph2d.constantline(Marker_Stim/1E2+(i-1)*var_stim(7)/1E3,'ydata', get(gca,'ylim'), 'color', 'black', 'LineStyle', ':');
changedependvar(hx,'x');
end
-hx2 = graph2d.constantline((Marker_Stim/1E2 -var_stim(8)/1E3), 'color', 'red');
-changedependvar(hx2,'x');
subplot(212), plot(timeaxis,Vt)
-title('Thalamic relay membrane voltage'), xlabel('time in s'), ylabel('Vt in mV')
-ylim(get(gca,'ylim'));
+title('Thalamic relay membrane voltage'),
+xlabel('Time in s'),
+ylabel('V_{t} in mV')
+ylim([-70,-35]);
% vertical line for markers
for i=1:var_stim(6)
hx = graph2d.constantline(Marker_Stim/1E2+(i-1)*var_stim(7)/1E3,'ydata', get(gca,'ylim'), 'color', 'black', 'LineStyle', ':');
changedependvar(hx,'x');
end
-% [Pxx,f] = pwelch(Ve-mean(Ve),hamming(L/30), 4*L/T, 2048, L/T);
-% n = find(f<=30, 1, 'last' );
-%
-% figure(2)
-% plot(f(1:n),log(Pxx(1:n)))
-% title('Powerspectrum with pwelch'), xlabel('frequency in Hz'), ylabel('Power (log)')
+[Pxx,f] = pwelch(Ve-mean(Ve),hamming(5*L/T), 2*L/T, [], L/T);
+n = find(f<=30, 1, 'last' );
+
+figure(2)
+plot(f(1:n),log(Pxx(1:n)))
+title('Powerspectrum with pwelch'), xlabel('frequency in Hz'), ylabel('Power (log)')
%save('Timeseries', 'Ve', 'Vt');
end
View
11 Thalamic_Column.cpp
@@ -160,10 +160,15 @@ double Thalamic_Column::m_inf_h (int N) const{
return h;
}
-/* Activation time for slow components in TC population after Destexhe 1993 */
+/* Activation time for slow components in TC population*/
double Thalamic_Column::tau_m_h (int N) const{
_SWITCH((Vt))
- double tau = 1. / (exp(-14.59 - 0.086 * var_Vt) + exp(-1.87 + 0.07 * var_Vt));
+ /* Destexhe 1993 */
+ //double tau = 1. / (exp(-14.59 - 0.086 * var_Vt) + exp(-1.87 + 0.07 * var_Vt));
+ /* Bazhenov1998 */
+ double tau = (5.3 + 267/(exp((var_Vt + 71.5)/14.2) + exp(-(var_Vt + 89)/11.6)));
+ /* Chen2012 */
+ //double tau = (20 +1000/(exp((var_Vt + 71.5)/14.2) + exp(-(var_Vt + 89)/11.6)));
return tau;
}
/****************************************************************************************************/
@@ -256,7 +261,7 @@ void Thalamic_Column::set_RK (int N) {
h_T_t [N] = dt*(h_inf_T_t(N) - var_h_T_t)/tau_h_T_t(N);
h_T_r [N] = dt*(h_inf_T_r(N) - var_h_T_r)/tau_h_T_r(N);
m_h [N] = dt*((m_inf_h(N) * (1 - var_m_h2) - var_m_h)/tau_m_h(N) - k3 * var_P_h * var_m_h + k4 * var_m_h2);
- m_h2 [N] = dt*(k3 * var_P_h * var_m_h - k4 * var_m_h2);
+ m_h2 [N] = dt*(k3 * k1 * pow(var_Ca, n_P)/(k1*pow(var_Ca, n_P)+k2) * var_m_h - k4 * var_m_h2);
P_h [N] = dt*(k1 * pow(var_Ca, n_P) * (1 - var_P_h) - k2 * var_P_h);
Phi_tt [N] = dt*(var_x_tt);
Phi_tr [N] = dt*(var_x_tr);
View
26 Thalamic_Column.h
@@ -57,8 +57,8 @@ class Thalamic_Column {
/* Constructor for simulation */
Thalamic_Column(double* Param, double* Con)
- : g_LK_t (Param[0]), g_LK_r(Param[1]), g_h(Param[2]),
- N_et (Con[0]), N_er (Con[1])
+ : g_h (Param[0]), g_LK_t (Param[1]), g_LK_r (Param[2]),
+ N_et (Con[0]), N_er (Con[1])
{set_RNG();}
/* Get the pointer to the cortical module */
@@ -155,8 +155,8 @@ class Thalamic_Column {
const double theta_r = -58.6;
/* Sigmoid gain in mV */
- const double sigma_t = 4;
- const double sigma_r = 4;
+ const double sigma_t = 6;
+ const double sigma_r = 6;
/* Scaling parameter for sigmoidal mapping (dimensionless) */
const double C1 = (3.14159265/sqrt(3));
@@ -174,15 +174,15 @@ class Thalamic_Column {
const double g_L_r = 1;
/* Potassium leak current */
- const double g_LK_t = 0.02;
- const double g_LK_r = 0.02;
+ const double g_LK_t = 0.024;
+ const double g_LK_r = 0.024;
/* T current */
const double g_T_t = 3;
const double g_T_r = 2.3;
/* h current */
- const double g_h = 0.05;
+ const double g_h = 0.048;
/* Reversal potentials in mV */
/* Synaptic */
@@ -203,9 +203,9 @@ class Thalamic_Column {
const double E_h = -40;
/* Calcium parameters */
- const double alpha_Ca = -52E-6; /* influx per spike in nmol */
+ const double alpha_Ca = -50E-6; /* influx per spike in nmol */
const double tau_Ca = 10; /* calcium time constant in ms */
- const double Ca_0 = 2.4E-4; /* resting concentration */
+ const double Ca_0 = 2E-4; /* resting concentration */
/* I_h activation parameters */
const double k1 = 2.5E7;
@@ -222,11 +222,11 @@ class Thalamic_Column {
/* Connectivities (dimensionless) */
- const double N_tr = 4;
+ const double N_tr = 3;
const double N_rt = 4;
- const double N_rr = 20;
- const double N_et = 10;
- const double N_er = 10;
+ const double N_rr = 22;
+ const double N_et = 5;
+ const double N_er = 5;
/* Pointer to cortical column */
Cortical_Column* Cortex;

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