//genesis
include MScell/globals_1 // Defines & initializes cell specific parameters
include clamps.g
int usingHsolve = 1
int usingNewKaF = 0
int usingNaP = 1
int addCa2Spine = 1
int useAMPA = 1
int use_F_factor = 1
int usingElectro_Leak = 0 // to simulate eletro-leak in the soma
int usingClamp = 0
int usingCaT = 1
int usingCaR = 1
int usingKIR = 1
int showMSoutput = 1
int usingSaturSynchan = 100 //3.3
/* F is the factor for spine compensation
*** you can ignore this part*******************/
if ({{use_F_factor}==1})
float F = 1.38 // 1.38
else
float F = 1
end
float F2 = 1 // RA in the distal dendrite = 4, Surmeier's paper
str neuronname = "/cell" // cell morphology file
include MScell/MScellSpine_test // access make_MS_cell this function is only called from MSsim.g
str pfile="MScell/swc5_SPN.g"
include xcell // access functions "record_channel"
// These two functions are only called from MSsim.g
/****************************** End includes *********************************/
float speedA = 20
setclock 0 {speedA*1e-6} // Simulation time step (Second)
setclock 1 {speedA*1e-6} // clock for graphic output
/******************* Compensate for spines***********************************/
make_MS_cell {neuronname} {pfile} 30.0e-6 160.0e-6 {F} {F2} // MS_cell.g
/*****************************************************************************************/
reset
/*****************************Visualize the neuron**********************************/
///////////////////////////////////////////////////////////////////////////////
str list = {findCompt {neuronname} 1e-6 200e-6 0.5e-6 }
increaseXcellDia {neuronname} {list} 2
create xform /cellform1 [620,50,1000,1000]
create xdraw /cellform1/draw [0,0,100%,100%] \
-wx 3e-3 \
-wy 3e-3 \
-transform ortho3d \
-bg black
//setfield {neuronname}/soma dia 8e-6
setfield /cellform1/draw xmin -1.2e-4 xmax 1.2e-4 ymin -1.2e-4 ymax 1.2e-4 \
zmin -1e-3 zmax 1e-3
setfield /cellform1/draw transform z
xshow /cellform1
echo creating xcell
create xcell /cellform1/draw/cell
setfield /cellform1/draw/cell colmin -0.09 colmax -0.01 \
path {neuronname}/##[TYPE=compartment] field Vm \
script "echo widget clicked on = <w> value = <v>" \
diarange -50
xcolorscale hot
str above = "cell"
str parent = "/cellform1/draw"
//make_colorbar {parent} {above}
reset
/////////////////////////////////////////////////////////////////////////////////////////
str compt_1 = "1409" //proximal,1146; distal,1409
add_spines {neuronname} {compt_1} spine 15 // located 90-100 um from the soma
// IMPORT!!!! Using HSOVLE METHOD HERE
if ({usingHsolve == 1})
pushe {neuronname}
create hsolve solve
setfield solve \
chanmode 1 \
path {neuronname}/##[][TYPE=compartment]
call ^ SETUP
setmethod 11
pope
reset
end
/****************************** End MSsim.g **********************************/
// // /********************************************************
// // ************* begin to draw results**********************
// // *********************************************************/
if({showMSoutput}==1)
/*****function make_xcells(xcell, label, title1,title2,title3,title4,tmin,tmax)********/
str xcell ="xcell"
str label = "Dendritic Plateau at "@{compt_1}
str title1 = "Membrane_Voltage"
str xcellPath = "output/"@{xcell}
int chanmode = 0
float tmin = 0.2
float tmax = 0.5
make_VerticalXcells {xcellPath} {label} {title1} {tmin} {tmax}
/*****************************************************************************/
/*********function record_channel(cellpath,compt,channel,xcell,title, color,ymin,ymax)********/
/*********function record_voltage (cellpath, compt, xcell,lable,color,ymin,ymax,chanmode)****/
/******************** record voltage ****************************************************/
float ymin_volt = -0.09
float ymax_volt = 0.0
record_voltage {neuronname} soma {xcellPath} {title1} "soma" "blue" {ymin_volt} {ymax_volt} {chanmode}
record_voltage {neuronname} {compt_1} {xcellPath} {title1} "dendrite" "red" {ymin_volt} {ymax_volt} {chanmode} // to record voltage of the compartment
//record_voltage {neuronname} 1437 {xcellPath} {title1} "distal tip" "black" {ymin_volt} {ymax_volt} {chanmode}
//record_voltage {neuronname} 746 {xcellPath} {title1} "another branch" "pink" {ymin_volt} {ymax_volt} {chanmode}
reset
/**************************************************************************/
end
mkdir /home/kai/results/Plateaus
float isi = 0.001
int inj = 100
float inj1 = inj*1e-12
// Simulation Protocols
setfield {neuronname}/soma inject {inj1}
step 0.3 -time // activation of 15 spines need 15 ms, "0.485"
activate_spines {neuronname} {compt_1} "spine" 15 {isi} 1
step 0.2 -time
//
//deletemsg /output/Vsoma 0 -in
//deletemsg /output/Vdend 0 -in
//reset
//end
//end // for n=...
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