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Fixed some of the parameters to get a better SO_Average for N2. However, 

the mean membrane voltageis rather high(-54 mV compared to -56.4 for
cortex only)
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1 parent 8385cf5 commit 7be127aa1ed12c5a7c0b838620244e01755b4a73 @miscco committed Jan 9, 2015
Unified Split
Showing with 131 additions and 121 deletions.
  1. +32 −32 Cortical_Column.h
  2. +14 −14 Plots.m
  3. +21 −16 Stimulation.h
  4. +3 −2 TC.cpp
  5. +1 −1 Thalamic_Column.cpp
  6. +53 −52 Thalamic_Column.h
  7. +3 −1 macros.h
  8. +4 −3 saves.h
View
64 Cortical_Column.h
@@ -65,40 +65,40 @@ class Cortical_Column {
/* Return axonal flux */
double get_phi (int N) const {_SWITCH((phi)); return var_phi;}
- /* Initialize the RNGs */
- void set_RNG (void);
+ /* Data storage access */
+ friend void get_data (int, Cortical_Column&, Thalamic_Column&, _REPEAT(double*, 4));
- /* Firing rates */
- double get_Qe (int) const;
- double get_Qi (int) const;
+ /* ODE functions */
+ void set_RK (int);
+ void add_RK (void);
- /* Currents */
- double I_ee (int) const;
- double I_ei (int) const;
- double I_ie (int) const;
- double I_ii (int) const;
- double I_L_e (int) const;
- double I_L_i (int) const;
- double I_KNa (int) const;
+ /* Stimulation protocol access */
+ friend class Stim;
- /* Potassium pump */
- double Na_pump (int) const;
+private:
+ /* Initialize the RNGs */
+ void set_RNG (void);
- /* Noise function */
- double noise_xRK (int, int) const;
+ /* Firing rates */
+ double get_Qe (int) const;
+ double get_Qi (int) const;
- /* ODE functions */
- void set_RK (int);
- void add_RK (void);
+ /* Currents */
+ double I_ee (int) const;
+ double I_ei (int) const;
+ double I_ie (int) const;
+ double I_ii (int) const;
+ double I_L_e (int) const;
+ double I_L_i (int) const;
+ double I_KNa (int) const;
- /* Data storage access */
- friend void get_data (int, Cortical_Column&, Thalamic_Column&, _REPEAT(double*, 4));
+ /* Potassium pump */
+ double Na_pump (int) const;
- /* Stimulation protocol access */
- friend class Stim;
+ /* Noise function */
+ double noise_xRK (int, int) const;
-private:
- /* Population variables */
+ /* Population variables */
vector<double> Ve = _INIT(E_L_e), /* excitatory membrane voltage */
Vi = _INIT(E_L_i), /* inhibitory membrane voltage */
Na = _INIT(Na_eq), /* Na concentration */
@@ -141,9 +141,9 @@ class Cortical_Column {
/* parameters of the firing adaption */
const double alpha_Na = 2; /* Sodium influx per spike in mM ms */
- const double tau_Na = 1.7; /* Sodium time constant in ms */
+ const double tau_Na = 2; /* Sodium time constant in ms */
- const double R_pump = 0.09; /* Na-K pump constant in mM/ms */
+ const double R_pump = 0.09; /* Na-K pump constant in mM/ms */
const double Na_eq = 9.5; /* Na-eq concentration in mM */
/* PSP rise time in ms^-1 */
@@ -174,14 +174,14 @@ class Cortical_Column {
/* Noise parameters in ms^-1 */
const double mphi = 0E-3;
- const double dphi = 60E-3;;
+ const double dphi = 60E-3;
double input = 0.0;
/* Connectivities (dimensionless) */
- const double N_ee = 120;
+ const double N_ee = 125;
const double N_ei = 72;
- const double N_ie = 90;
- const double N_ii = 90;
+ const double N_ie = 100;
+ const double N_ii = 100;
const double N_te = 0;
const double N_ti = 0;
View
28 Plots.m
@@ -1,31 +1,31 @@
% mex command is given by:
-% mex CXXFLAGS="\$CXXFLAGS -std=c++11 -O3" TC.cpp Cortical_Column.cpp Thalamic_Column.cpp
+% mex CXXFLAGS="\$CXXFLAGS -std=c++11 -O3 -lgopm" TC.cpp Cortical_Column.cpp Thalamic_Column.cpp
function Plots(type)
if nargin == 0
- type = 2;
+ type = 1;
end
if type == 1
Param_Cortex = [4.7; % sigma_e
- 1.33; % g_KNa
+ 1.43; % g_KNa
120E-3]; % dphi
Param_Thalamus = [0.051; % g_h
0.024]; % g_LK
else
- Param_Cortex = [6.; % sigma_e
- 2.1; % g_KNa
+ Param_Cortex = [6; % sigma_e
+ 2.15; % g_KNa
120E-3]; % dphi
Param_Thalamus = [0.051; % g_h
- 0.02]; % g_LK
+ 0.02]; % g_LK
end
-Connectivity = [ 2.5; % N_et
- 2.5; % N_er
+Connectivity = [ 2.5; % N_et
+ 2.5; % N_er
6; % N_te
- 15]; % N_ti
+ 15]; % N_ti
% stimulation parameters
% first number is the mode of stimulation
@@ -34,11 +34,11 @@ function Plots(type)
% 2 == phase dependend
var_stim = [ 0; % mode of stimulation
- 300; % strength of the stimulus in Hz (spikes per second)
+ 60; % 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
+ 3; % Number of stimuli per event
1050; % time between stimuli within a event in ms
450]; % time until stimuli after minimum in ms
@@ -49,7 +49,7 @@ function Plots(type)
L = length(Vt);
timeaxis = linspace(0,T,L);
-figure(1)
+%figure(1)
subplot(411), plot(timeaxis,Ve)
title('Pyramidal membrane voltage'),
xlabel('Time in s'),
@@ -58,8 +58,8 @@ function Plots(type)
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'),'xdata', get(gca,'xlim'), 'color', 'black', 'LineStyle', ':');
- changedependvar(hx,'x');
+ %hx = graph2d.constantline(Marker_Stim/1E2+(i-1)*var_stim(7)/1E3,'ydata', get(gca,'ylim'),'xdata', get(gca,'xlim'), 'color', 'black', 'LineStyle', ':');
+ %changedependvar(hx,'x');
end
subplot(412), plot(timeaxis,Vt)
View
37 Stimulation.h
@@ -105,8 +105,11 @@ class Stim {
/* If a stimulation event has occurred and there is a minimal time (pause) until the next one */
bool stimulation_paused = false;
+ /* If burst mode is enabled */
+ bool burst_enabled = false;
+
/* In case of bursted stimulation start the bursts */
- bool burst_started = false;
+ bool burst_started = true;
/* Length of a burst stimulus */
int burst_length = 10;
@@ -183,8 +186,8 @@ void Stim::setup (double* var_stim) {
time_between_stimuli = (int) var_stim[6] * res / 1000;
/* Scale the length of burst_length and burst_ISI from ms to dt*/
- burst_length = (int) 6 * res / 1000;
- burst_ISI = (int) 44 * res / 1000;
+ burst_length = (int) 2 * res / 1000;
+ burst_ISI = (int) 28 * res / 1000;
/* If ISI is fixed do not create RNG */
if (mode == 1) {
@@ -310,19 +313,21 @@ void Stim::check_stim (int time) {
count_bursts++;
/* Switch stimulation on and off wrt burst parameters */
- if(burst_started) {
- if(count_bursts%burst_length==0) {
- count_bursts = 0;
- burst_started = false;
- Thalamus->set_input(0.0);
- }
- } else {
- if(count_bursts%burst_ISI==0) {
- count_bursts = 0;
- burst_started = true;
- Thalamus->set_input(strength);
- }
- }
+ if(burst_enabled) {
+ if(burst_started) {
+ if(count_bursts%burst_length==0) {
+ count_bursts = 0;
+ burst_started = false;
+ Thalamus->set_input(0.0);
+ }
+ } else {
+ if(count_bursts%burst_ISI==0) {
+ count_bursts = 0;
+ burst_started = true;
+ Thalamus->set_input(strength);
+ }
+ }
+ }
}
/* Wait if there is a pause between stimulation events */
View
5 TC.cpp
@@ -103,8 +103,9 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
plhs[1] = Vt;
plhs[2] = Ca;
plhs[3] = ah;
- plhs[4] = Stimulation.get_marker();
-return;
+ plhs[4] = Stimulation.get_marker();
+
+ return;
}
/****************************************************************************************************/
/* end */
View
2 Thalamic_Column.cpp
@@ -51,7 +51,7 @@ void Thalamic_Column::set_RNG(void) {
/****************************************************************************************************/
/* Thalamic relay (TC) firing rate */
double Thalamic_Column::get_Qt (int N) const{
- _SWITCH((Vt))
+ _SWITCH((Vt))
double q = Qt_max/ (1 + exp(-C1 * (var_Vt - theta_t) / sigma_t));
return q;
}
View
105 Thalamic_Column.h
@@ -61,63 +61,64 @@ class Thalamic_Column {
N_et (Con[0]), N_er (Con[1])
{set_RNG();}
- /* Get the pointer to the cortical module */
- void get_Cortex (Cortical_Column& C) {Cortex = &C;}
-
- /* Set strength of input */
- void set_input (double I) {input = I;}
-
- /* Get axonal flux */
- double get_phi (int N) const {_SWITCH((phi)); return var_phi;}
-
- /* Initialize the RNGs */
- void set_RNG (void);
-
- /* Firing rates */
- double get_Qt (int) const;
- double get_Qr (int) const;
-
- /* Synaptic currents */
- double I_et (int) const;
- double I_it (int) const;
- double I_er (int) const;
- double I_ir (int) const;
-
- /* Activation functions */
- double m_inf_T_t (int) const;
- double m_inf_T_r (int) const;
- double m_inf_h (int) const;
- double tau_m_h (int) const;
- double P_H (int) const;
- double act_h (void)const;
-
- /* Deactivation functions */
- double h_inf_T_t (int) const;
- double h_inf_T_r (int) const;
- double tau_h_T_t (int) const;
- double tau_h_T_r (int) const;
-
- /* Currents */
- double I_L_t (int) const;
- double I_L_r (int) const;
- double I_LK_t (int) const;
- double I_LK_r (int) const;
- double I_T_t (int) const;
- double I_T_r (int) const;
- double I_h (int) const;
-
- /* Noise functions */
- double noise_xRK (int) const;
-
- /* ODE functions */
- void set_RK (int);
- void add_RK (void);
+ /* Get the pointer to the cortical module */
+ void get_Cortex (Cortical_Column& C) {Cortex = &C;}
+
+ /* Get axonal flux */
+ double get_phi (int N) const {_SWITCH((phi)); return var_phi;}
+
+ /* ODE functions */
+ void set_RK (int);
+ void add_RK (void);
/* Data storage access */
friend void get_data (int, Cortical_Column&, Thalamic_Column&, _REPEAT(double*, 4));
+ /* Set strength of input */
+ void set_input (double I) {input = I;}
+
private:
- /* Population variables */
+
+ /* Initialize the RNGs */
+ void set_RNG (void);
+
+ /* Firing rates */
+ double get_Qt (int) const;
+ double get_Qr (int) const;
+
+ /* Synaptic currents */
+ double I_et (int) const;
+ double I_it (int) const;
+ double I_er (int) const;
+ double I_ir (int) const;
+
+ /* Activation functions */
+ double m_inf_T_t (int) const;
+ double m_inf_T_r (int) const;
+ double m_inf_h (int) const;
+ double tau_m_h (int) const;
+ double P_H (int) const;
+ double act_h (void)const;
+
+ /* Deactivation functions */
+ double h_inf_T_t (int) const;
+ double h_inf_T_r (int) const;
+ double tau_h_T_t (int) const;
+ double tau_h_T_r (int) const;
+
+ /* Currents */
+ double I_L_t (int) const;
+ double I_L_r (int) const;
+ double I_LK_t (int) const;
+ double I_LK_r (int) const;
+ double I_T_t (int) const;
+ double I_T_r (int) const;
+ double I_h (int) const;
+
+ /* Noise functions */
+ double noise_xRK (int) const;
+
+ /* Population variables */
vector<double> Vt = _INIT(E_L_t), /* TC membrane voltage */
Vr = _INIT(E_L_r), /* RE membrane voltage */
Ca = _INIT(Ca_0), /* Calcium concentration of TC population */
View
4 macros.h
@@ -23,7 +23,8 @@
/****************************************************************************************************/
/* Definition of all macros used */
/****************************************************************************************************/
-#pragma once
+#ifndef MACROS_H
+#define MACROS_H
#include <boost/preprocessor/cat.hpp>
#include <boost/preprocessor/punctuation/comma_if.hpp>
#include <boost/preprocessor/repetition/repeat.hpp>
@@ -79,3 +80,4 @@
/****************************************************************************************************/
/* end */
/****************************************************************************************************/
+#endif // MACROS_H
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