{ "metadata": { "name": "" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "code", "collapsed": false, "input": [ "####Glutamate Stimulation-will be used for normalization####\n", "import pickle\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", "import random\n", "from neuron import h,gui\n", "\n", "####Sections and Connections####\n", "nofsections = 27 # 1soma + 25dendritic sections + 1terminating section \n", "nofspines =1 # number of spines is 1 throughout this simulation\n", "\n", "gc=[h.Section() for i in range(nofsections)]\n", "spineh=[h.Section() for i in range(nofspines)]\n", "spinen=[h.Section() for i in range(nofspines)]\n", "\n", "for i in range(nofsections-1):\n", " gc[i+1].connect(gc[i],1,0)\n", "for i in range(nofspines):\n", " spineh[i].connect(spinen[i],0,1)\n", " \n", "j=0\n", "for i in range(nofspines): #spines start at 100um from soma, on 11th dendritic section\n", " spinen[i].connect(gc[11+j],0.5,1)\n", " j=j+1\n", " \n", "####Morphology and other Parameters#### \n", "h.celsius=22 #temperature\n", "h.dt=0.025 #temporal resolution,ms\n", "\n", "for i in range(nofsections): \n", " gc[i].L=10 #dendrite total length is 260 um\n", " gc[i].nseg=3\n", " gc[i].Ra=200\n", " \n", "gc[0].diam=10 #soma size is 10umx10um, and there are two tapering regimes:\n", "for i in range(1,11):#1.tapering starts at 2.35um, ends at 1.7um , first 10 sections as in Ona-Jodar et al. Front Cell Neurosci 2017 \n", " gc[i].diam=2.35-(i-1)*((2.35-1.7)/9)\n", "for i in range(11,27):#2.tapering starts at 1.7um ends at 1.2um, next 15 sections \n", " gc[i].diam=1.7-(i-10)*((1.7-1.2)/16)\n", " \n", "for i in range(nofspines): \n", " spineh[i].diam=1\n", " spinen[i].diam=0.3 \n", " spineh[i].L=1\n", " spinen[i].L=2.5\n", " spineh[i].nseg=3\n", " spinen[i].nseg=3\n", " spinen[i].Ra=4.9e3 #Ra is normalized as ohmcm.\n", " \n", "presyn=h.Section() #with all other default specifications\n", "presyn.L=10\n", "presyn.diam=10\n", "\n", "####Settings for Ion channels and Synaptic Receptors and their Parameters#### \n", "for i in range(nofsections):\n", " gc[i].insert('constant')#dummy current source\n", " gc[i].insert('cadifusnpumpOGBenddif')#ca2+ and buffers diffusion,ca2+ pumps \n", " gc[i].insert('nax')\n", " gc[i].insert('kamt')\n", " gc[i].insert('pas')\n", " gc[i].g_pas=6e-4 \n", " gc[i].e_pas=-85\n", " gc[i].gbar_nax=0.5\n", " gc[i].gbar_kamt=0.01\n", " gc[i].cm=1\n", " \n", " gc[i].insert('canhem')#HVA Ca2+ channel \n", " gc[i].insert('cathem')#T-type Ca2+ channel\n", " gc[i].q10_cathem=3\n", " gc[i].q10_canhem=3 \n", " gc[i].a0m_cathem=0.055633 #to adjust the opening rate\n", " gc[i].a0m_canhem=0.331432 #to adjust the opening rate \n", " gc[i].gcanbar_canhem=0.0005\n", " gc[i].gcatbar_cathem=0.0003\n", " \n", " gc[i].TotalPump_cadifusnpumpOGBenddif=2e-11 \n", " \n", "for i in range(nofspines): \n", " spineh[i].insert('constant')#dummy current source\n", " spineh[i].insert('cadifusnpumpOGBenddif')#ca2+ and buffers diffusion,ca2+ pumps \n", " spineh[i].insert('nax')\n", " spineh[i].insert('kamt')\n", " spineh[i].insert('pas')\n", " spineh[i].gbar_nax=0.5 \n", " spineh[i].gbar_kamt=0.01\n", " spineh[i].g_pas=2e-4\n", " spineh[i].e_pas=-85\n", " spineh[i].cm=1\n", "\n", " spineh[i].insert('canhem')\n", " spineh[i].insert('cathem')\n", " spineh[i].q10_canhem=3\n", " spineh[i].q10_cathem=3\n", " spineh[i].a0m_cathem=0.055633 #to adjust the opening rate\n", " spineh[i].a0m_canhem=0.331432 #to adjust the opening rate\n", " \n", " spineh[i].gcanbar_canhem=0.0004 \n", " \n", " spineh[i].TotalPump_cadifusnpumpOGBenddif=2.2e-11 \n", " \n", "AMPARsyn=[h.AMPA5() for i in range(nofspines)]\n", "NMDARsyn=[h.NMDA5() for i in range(nofspines)]\n", "\n", "for i in range(nofspines): \n", " AMPARsyn[i].loc(spineh[i](0.3))\n", " AMPARsyn[i].gmax=2000\n", " NMDARsyn[i].loc(spineh[i](0.7))\n", " NMDARsyn[i].gmax=383 \n", " NMDARsyn[i].gmax_ca=17 \n", " ##NMDAR Setting##\n", " NMDARsyn[i].Rb= 5e-3\n", " NMDARsyn[i].Ru=12.9e-3\n", " NMDARsyn[i].Rd=8.4e-3\n", " NMDARsyn[i].Rr=6.8e-3\n", " NMDARsyn[i].Ro=46.5e-3\n", " NMDARsyn[i].Rc=73.8e-3 \n", " ####\n", " spinen[i].insert('cadifusnpumpOGBenddif')\n", " spinen[i].TotalPump_cadifusnpumpOGBenddif=0 #there is no active mechanism on the neck\n", "\n", "####Setting Ca Dynamic Global Parameters####\n", "h.DCa_cadifusnpumpOGBenddif=0.6\n", "h.mg_NMDA5=1\n", "##endogenous buffer\n", "for i in range(nofsections):\n", " gc[i].k1buf1_cadifusnpumpOGBenddif=1000\n", " gc[i].k2buf1_cadifusnpumpOGBenddif=1\n", " gc[i].TotalBuffer1_cadifusnpumpOGBenddif=0.12\n", "for i in range(nofspines):\n", " spineh[i].k1buf1_cadifusnpumpOGBenddif=1000\n", " spineh[i].k2buf1_cadifusnpumpOGBenddif=1\n", " spineh[i].TotalBuffer1_cadifusnpumpOGBenddif=0.12\n", "##exogenous buffer \n", "for i in range(nofsections):\n", " gc[i].k1buf2_cadifusnpumpOGBenddif=1000\n", " gc[i].k2buf2_cadifusnpumpOGBenddif=0.2\n", " gc[i].TotalBuffer2_cadifusnpumpOGBenddif=0.1 #for \"no OGB case\", set this to 0\n", "for i in range(nofspines):\n", " spineh[i].k1buf2_cadifusnpumpOGBenddif=1000\n", " spineh[i].k2buf2_cadifusnpumpOGBenddif=0.2\n", " spineh[i].TotalBuffer2_cadifusnpumpOGBenddif=0.1 #for \"no OGB case\", set this to 0\n", "\n", "####Mapping of Ca Concentration to fluorescence signal df/f \u2013 based on experimental data and simulations, see Figure 3C; not valid for \"no OGB case\"####\n", "def spine_fit(x):\n", " y = 14390070 + (-49.1502 - 14390070)/(1 + (x/6632796000)**0.6715641)\n", " return y\n", " \n", "def dend_fit(x): #not calculated and used based on experiment\n", " y = 14390070 + (-49.1502 - 14390070)/(1 + (x/6632796000)**0.6715641)\n", " return y\n", "\n", "####Simulation Readout####\n", "time_h = h.Vector()\n", "time_h.record(h._ref_t)\n", "vrec_gc=[h.Vector() for i in range(nofsections)] #gc[0] is the soma, gc[10] is the 1th parent dendrite\n", "vrec_spineh=[h.Vector() for i in range(nofspines)] \n", "icaspineh=[h.Vector() for i in range(nofspines)] #overall influx\n", "ccaspineh=[h.Vector() for i in range(nofspines)] #overall concentration\n", "icagc=[h.Vector() for i in range(nofsections)] #overall influx\n", "ccagc=[h.Vector() for i in range(nofsections)] #overall concentration\n", "\n", "icanmdr=[h.Vector() for i in range(nofspines)]\n", "icahvacc=[h.Vector() for i in range(nofspines)]\n", "icattype=[h.Vector() for i in range(nofspines)]\n", "\n", "for i in range(nofsections): \n", " vrec_gc[i].record(gc[i](0.5)._ref_v)\n", "for i in range(nofspines): \n", " vrec_spineh[i].record(spineh[i](0.5)._ref_v) \n", "\n", "for i in range(nofspines): \n", " icahvacc[i].record(spineh[i](0.5)._ref_ica_canhem)\n", " icanmdr[i].record(NMDARsyn[i]._ref_ica)\n", " icattype[i].record(spineh[i](0.5)._ref_ica_cathem)\n", " \n", " icaspineh[i].record(spineh[i](0.5)._ref_ica)\n", " ccaspineh[i].record(spineh[i](0.5)._ref_caiav_cadifusnpumpOGBenddif) \n", " \n", "for i in range(nofsections):\n", " icagc[i].record(gc[i](0.5)._ref_ica)\n", " ccagc[i].record(gc[i](0.5)._ref_caiav_cadifusnpumpOGBenddif) \n", " \n", "icanmdr_show=[np.array for i in range(nofspines)]\n", "icattype_show=[np.array for i in range(nofspines)]\n", "icahvacc_show=[np.array for i in range(nofspines)]\n", "ccaspineh_show=[np.array for i in range(nofspines)]\n", "icaspineh_show=[np.array for i in range(nofspines)]\n", "ccagc_show=[np.array for i in range(nofsections)]\n", "icagc_show=[np.array for i in range(nofsections)] \n", "\n", "icanmdr_show=[np.array for i in range(nofspines)]\n", "icattype_show=[np.array for i in range(nofspines)]\n", "icahvacc_show=[np.array for i in range(nofspines)]\n", "y_dff_spineh=[np.array for i in range(nofspines)]\n", "y_dff_gc=[np.array for i in range(nofsections)]\n", "v_dend=[np.array for i in range(nofsections)]\n", "v_spineh=[np.array for i in range(nofspines)]\n", "\n", "gcattype_vec=[float for i in range(30)]\n", "\n", "vmspine_obj_glu=open(\"vmspine_0_record_glu\",\"w\")\n", "caspine_0_obj_glu=open(\"caspine_0_record_glu\",\"w\")\n", "dffspine_0_obj_glu=open(\"dffspine_0_record_glu\",\"w\")\n", "cagc_obj_glu=open(\"cagc_glu\",\"w\")\n", "dffgc_obj_glu=open(\"dffgc_glu\",\"w\")\n", " \n", "ittype_obj_glu=open(\"ittype_glu\",\"w\")\n", "ihvacc_obj_glu=open(\"ihvacc_glu\",\"w\")\n", "inmdr_obj_glu=open(\"inmdr_glu\",\"w\")\n", "\n", "gcattype_obj=open(\"gcattype_file\",\"w\")\n", "\n", "gcattype=0.00015 \n", "t_c=[0]\n", "for tc in t_c:\n", " for var in range(30): \n", " \n", "####Setting Stimulation####\n", "#Glutamate\n", " Rel=h.STEP_REL(0.75,presyn)\n", " Rel.amplitude=1 \n", " Rel.duration=3\n", " Rel.release_time=120\n", "\n", " for i in range(nofspines):\n", " h.setpointer(Rel._ref_GLU,'C',AMPARsyn[i])\n", " h.setpointer(Rel._ref_GLU,'C',NMDARsyn[i])\n", " \n", "####Running the Simulation####\n", " h.v_init=-85 #forced resting Vm for granule cells\n", " h.init()\n", "\n", " for l in range(nofsections):# dummy current source to compensate current caused by the forced Vm. \n", " gc[l].ic_constant=-(gc[l].ina+gc[l].ik+gc[l].ica)\n", " for l in range(nofspines): \n", " spineh[l].ic_constant=-(spineh[l].ina+spineh[l].ik+spineh[l].ica)\n", "\n", " if h.cvode.active():\n", " h.cvode.re_init()\n", " else:\n", " h.fcurrent()\n", " \n", " for i in range(nofspines): \n", " spineh[i].gcatbar_cathem=random.uniform(gcattype-0.5*gcattype,gcattype+gcattype) \n", " gcattype_vec[var]=spinen[0].gcatbar_cathem\n", " \n", " h.tstop =350\n", " h.run()\n", " \n", "#### Vectors and conversion of units (um to nm)####\n", " for i in range(nofspines):\n", " v_spineh[i]=np.asarray(vrec_spineh[i])\n", " ccaspineh_show[i]=1e6*np.asarray(ccaspineh[i])#converting to nM\n", " icanmdr_show[i]=(1e2*np.asarray(icanmdr[i]))/3.14 #converting nA to mA/cm2, spine area is (piXe-8)cm2 \n", " icahvacc_show[i]=np.asarray(icahvacc[i]) #mA/cm2\n", " icattype_show[i]=np.asarray(icattype[i]) #mA/cm2\n", " \n", " for i in range(nofsections):\n", " v_dend[i]=np.asarray(vrec_gc[i])\n", " ccagc_show[i]=1e6*np.asarray(ccagc[i])#converting to nM\n", "\n", "####Mapping of Ca Concentration to df/f####\n", " for i in range(nofspines): \n", " y_dff_spineh[i]=spine_fit(ccaspineh_show[i])\n", " \n", " for i in range(nofsections): \n", " y_dff_gc[i]=spine_fit(ccagc_show[i]) \n", " \n", " pickle.dump(v_spineh[0],vmspine_obj_glu)\n", " pickle.dump(ccaspineh_show[0],caspine_0_obj_glu)\n", " pickle.dump(y_dff_spineh[0],dffspine_0_obj_glu)\n", " pickle.dump(ccagc_show[11],cagc_obj_glu)\n", " pickle.dump(y_dff_gc[11],dffgc_obj_glu)\n", " \n", " pickle.dump(icattype_show[0],ittype_obj_glu)\n", " pickle.dump(icahvacc_show[0],ihvacc_obj_glu)\n", " pickle.dump(icanmdr_show[0],inmdr_obj_glu)\n", " \n", "pickle.dump(gcattype_vec,gcattype_obj)\n", "\n", "caspine_0_obj_glu.close()\n", "dffspine_0_obj_glu.close()\n", "vmspine_obj_glu.close()\n", "cagc_obj_glu.close()\n", "dffgc_obj_glu.close()\n", "\n", "ittype_obj_glu.close()\n", "ihvacc_obj_glu.close()\n", "inmdr_obj_glu.close()\n", "\n", "gcattype_obj.close()\n", "\n", "print \"run the next block\"" ], "language": "python", "metadata": {}, "outputs": [ { "ename": "KeyboardInterrupt", "evalue": "", "output_type": "pyerr", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)", "\u001b[0;32m<ipython-input-2-5c3a794cf8c3>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 267\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 268\u001b[0m \u001b[0mh\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtstop\u001b[0m \u001b[0;34m=\u001b[0m\u001b[0;36m350\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 269\u001b[0;31m \u001b[0mh\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 270\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 271\u001b[0m \u001b[0;31m#### Vectors and conversion of units (um to nm)####\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;31mKeyboardInterrupt\u001b[0m: " ] } ], "prompt_number": 2 }, { "cell_type": "code", "collapsed": false, "input": [ "####Current Clamp (global AP) Stimulation-will be used for normalization####\n", "\n", "import pickle\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", "from neuron import h,gui\n", "\n", "####Sections and Connections####\n", "nofsections = 27 # 1soma + 25dendritic sections + 1terminating section \n", "nofspines =1 # number of spines is 1 throughout this simulation\n", "\n", "gc=[h.Section() for i in range(nofsections)]\n", "spineh=[h.Section() for i in range(nofspines)]\n", "spinen=[h.Section() for i in range(nofspines)]\n", "\n", "for i in range(nofsections-1):\n", " gc[i+1].connect(gc[i],1,0)\n", "for i in range(nofspines):\n", " spineh[i].connect(spinen[i],0,1)\n", " \n", "j=0\n", "for i in range(nofspines): #spines start at 100um from soma, on 11th dendritic section\n", " spinen[i].connect(gc[11+j],0.5,1)\n", " j=j+1\n", " \n", "####Morphology and other Parameters#### \n", "h.celsius=22 #temperature\n", "h.dt=0.025 #temporal resolution,ms\n", "\n", "for i in range(nofsections): \n", " gc[i].L=10 #dendrite total length is 260 um\n", " gc[i].nseg=3\n", " gc[i].Ra=200\n", " \n", "gc[0].diam=10 #soma size is 10umx10um, and there are two tapering regimes:\n", "for i in range(1,11):#1.tapering starts at 2.35um, ends at 1.7um , first 10 sections as in Ona-Jodar et al. Front Cell Neurosci 2017 \n", " gc[i].diam=2.35-(i-1)*((2.35-1.7)/9)\n", "for i in range(11,27):#2.tapering starts at 1.7um ends at 1.2um, next 15 sections \n", " gc[i].diam=1.7-(i-10)*((1.7-1.2)/16)\n", " \n", "for i in range(nofspines): \n", " spineh[i].diam=1\n", " spinen[i].diam=0.3 \n", " spineh[i].L=1\n", " spinen[i].L=2.5\n", " spineh[i].nseg=3\n", " spinen[i].nseg=3\n", " spinen[i].Ra=4.9e3 #Ra is normalized as ohmcm.\n", " \n", "presyn=h.Section() #with all other default specifications\n", "presyn.L=10\n", "presyn.diam=10\n", "\n", "####Settings for Ion channels and Synaptic Receptors and their Parameters#### \n", "for i in range(nofsections):\n", " gc[i].insert('constant')#dummy current source\n", " gc[i].insert('cadifusnpumpOGBenddif')#ca and buffers diffusion,ca pumps \n", " gc[i].insert('nax')\n", " gc[i].insert('kamt')\n", " gc[i].insert('pas')\n", " gc[i].g_pas=6e-4 \n", " gc[i].e_pas=-85\n", " gc[i].gbar_nax=0.5\n", " gc[i].gbar_kamt=0.01\n", " gc[i].cm=1\n", " \n", " gc[i].insert('canhem')#HVA Ca2+ channel \n", " gc[i].insert('cathem')#T-type Ca2+ channel\n", " gc[i].q10_cathem=3\n", " gc[i].q10_canhem=3 \n", " gc[i].a0m_cathem=0.055633 #to adjust the opening rate\n", " gc[i].a0m_canhem=0.331432 #to adjust the opening rate \n", " gc[i].gcanbar_canhem=0.0005\n", " gc[i].gcatbar_cathem=0.0003\n", " \n", " gc[i].TotalPump_cadifusnpumpOGBenddif=2e-11 \n", " \n", "for i in range(nofspines): \n", " spineh[i].insert('constant')#dummy current source\n", " spineh[i].insert('cadifusnpumpOGBenddif')#ca and buffers diffusion,ca pumps \n", " spineh[i].insert('nax')\n", " spineh[i].insert('kamt')\n", " spineh[i].insert('pas')\n", " spineh[i].gbar_nax=0.5 \n", " spineh[i].gbar_kamt=0.01\n", " spineh[i].g_pas=2e-4\n", " spineh[i].e_pas=-85\n", " spineh[i].cm=1\n", "\n", " spineh[i].insert('canhem')\n", " spineh[i].insert('cathem')\n", " spineh[i].q10_canhem=3\n", " spineh[i].q10_cathem=3\n", " spineh[i].a0m_cathem=0.055633 #to adjust the opening rate\n", " spineh[i].a0m_canhem=0.331432 #to adjust the opening rate\n", " \n", " spineh[i].gcanbar_canhem=0.0004 \n", "\n", " spineh[i].TotalPump_cadifusnpumpOGBenddif=2.2e-11 \n", " \n", "AMPARsyn=[h.AMPA5() for i in range(nofspines)]\n", "NMDARsyn=[h.NMDA5() for i in range(nofspines)]\n", "\n", "for i in range(nofspines): \n", " AMPARsyn[i].loc(spineh[i](0.3))\n", " AMPARsyn[i].gmax=2000\n", " NMDARsyn[i].loc(spineh[i](0.7))\n", " NMDARsyn[i].gmax=383 \n", " NMDARsyn[i].gmax_ca=17 \n", " ##NMDAR Setting##\n", " NMDARsyn[i].Rb= 5e-3\n", " NMDARsyn[i].Ru=12.9e-3\n", " NMDARsyn[i].Rd=8.4e-3\n", " NMDARsyn[i].Rr=6.8e-3\n", " NMDARsyn[i].Ro=46.5e-3\n", " NMDARsyn[i].Rc=73.8e-3 \n", " ####\n", " spinen[i].insert('cadifusnpumpOGBenddif')\n", " spinen[i].TotalPump_cadifusnpumpOGBenddif=0 #there is no active mechanism on the neck\n", "\n", "####Setting Ca Dynamic Global Parameters####\n", "h.DCa_cadifusnpumpOGBenddif=0.6\n", "h.mg_NMDA5=1\n", "##endogenous buffer\n", "for i in range(nofsections):\n", " gc[i].k1buf1_cadifusnpumpOGBenddif=1000\n", " gc[i].k2buf1_cadifusnpumpOGBenddif=1\n", " gc[i].TotalBuffer1_cadifusnpumpOGBenddif=0.12\n", "for i in range(nofspines):\n", " spineh[i].k1buf1_cadifusnpumpOGBenddif=1000\n", " spineh[i].k2buf1_cadifusnpumpOGBenddif=1\n", " spineh[i].TotalBuffer1_cadifusnpumpOGBenddif=0.12\n", "##exogenous buffer \n", "for i in range(nofsections):\n", " gc[i].k1buf2_cadifusnpumpOGBenddif=1000\n", " gc[i].k2buf2_cadifusnpumpOGBenddif=0.2\n", " gc[i].TotalBuffer2_cadifusnpumpOGBenddif=0.1 #for \"no OGB case\", set this to 0\n", "for i in range(nofspines):\n", " spineh[i].k1buf2_cadifusnpumpOGBenddif=1000\n", " spineh[i].k2buf2_cadifusnpumpOGBenddif=0.2\n", " spineh[i].TotalBuffer2_cadifusnpumpOGBenddif=0.1 #for \"no OGB case\", set this to 0\n", "\n", "####Mapping of Ca Concentration to fluorescence signal df/f \u2013 based on experimental data and simulations, see Figure 3C; not valid for \"no OGB case\"####\n", "def spine_fit(x):\n", " y = 14390070 + (-49.1502 - 14390070)/(1 + (x/6632796000)**0.6715641)\n", " return y\n", " \n", "def dend_fit(x): #not calculated and used based on experiment\n", " y = 14390070 + (-49.1502 - 14390070)/(1 + (x/6632796000)**0.6715641)\n", " return y\n", "\n", "####Simulation Readout####\n", "time_h = h.Vector()\n", "time_h.record(h._ref_t)\n", "vrec_gc=[h.Vector() for i in range(nofsections)] #gc[0] is the soma, gc[10] is the 1th parent dendrite\n", "vrec_spineh=[h.Vector() for i in range(nofspines)] \n", "icaspineh=[h.Vector() for i in range(nofspines)] #overall influx\n", "ccaspineh=[h.Vector() for i in range(nofspines)] #overall concentration\n", "icagc=[h.Vector() for i in range(nofsections)] #overall influx\n", "ccagc=[h.Vector() for i in range(nofsections)] #overall concentration\n", "\n", "icahvacc=[h.Vector() for i in range(nofspines)]\n", "icattype=[h.Vector() for i in range(nofspines)]\n", "\n", "for i in range(nofsections): \n", " vrec_gc[i].record(gc[i](0.5)._ref_v)\n", "for i in range(nofspines): \n", " vrec_spineh[i].record(spineh[i](0.5)._ref_v) \n", "\n", "for i in range(nofspines): \n", " icahvacc[i].record(spineh[i](0.5)._ref_ica_canhem)\n", " icattype[i].record(spineh[i](0.5)._ref_ica_cathem)\n", " \n", " icaspineh[i].record(spineh[i](0.5)._ref_ica)\n", " ccaspineh[i].record(spineh[i](0.5)._ref_caiav_cadifusnpumpOGBenddif) \n", " \n", "for i in range(nofsections):\n", " icagc[i].record(gc[i](0.5)._ref_ica)\n", " ccagc[i].record(gc[i](0.5)._ref_caiav_cadifusnpumpOGBenddif) \n", " \n", "icattype_show=[np.array for i in range(nofspines)]\n", "icahvacc_show=[np.array for i in range(nofspines)]\n", "ccaspineh_show=[np.array for i in range(nofspines)]\n", "icaspineh_show=[np.array for i in range(nofspines)]\n", "ccagc_show=[np.array for i in range(nofsections)]\n", "icagc_show=[np.array for i in range(nofsections)] \n", "\n", "icattype_show=[np.array for i in range(nofspines)]\n", "icahvacc_show=[np.array for i in range(nofspines)]\n", "y_dff_spineh=[np.array for i in range(nofspines)]\n", "y_dff_gc=[np.array for i in range(nofsections)]\n", "v_dend=[np.array for i in range(nofsections)]\n", "v_spineh=[np.array for i in range(nofspines)]\n", "\n", "vmspine_obj_ap=open(\"vmspine_0_record_ap\",\"w\")\n", "caspine_0_obj_ap=open(\"caspine_0_record_ap\",\"w\")\n", "dffspine_0_obj_ap=open(\"dffspine_0_record_ap\",\"w\")\n", "cagc_obj_ap=open(\"cagc_ap\",\"w\")\n", "dffgc_obj_ap=open(\"dffgc_ap\",\"w\")\n", " \n", "ittype_obj_ap=open(\"ittype_ap\",\"w\")\n", "ihvacc_obj_ap=open(\"ihvacc_ap\",\"w\")\n", "\n", "t_c=[-100,-80,-60,-40,-20,-12,-10,-8,-7,-6,-5,-4,-3,-2,0,2,3,4,5,6,7,8,10,12,20,40,60,80,100]\n", "for tc in t_c:\n", " for var in range(30):\n", "####Setting Stimulation####\n", "#Current Clamp (Global AP)\n", " APstim1=h.IClamp(0.5,sec=gc[0])\n", " APstim1.delay=120+tc #mS\n", " APstim1.dur=3 #mS\n", " APstim1.amp=1 #nA\n", "#Glutamate-not applicable in this block, just mentioned to avoid pointer problem.amplitude=0 \n", " Rel=h.STEP_REL(0.75,presyn)\n", " Rel.amplitude=0\n", " Rel.duration=3\n", " Rel.release_time=120\n", "\n", " for i in range(nofspines):\n", " h.setpointer(Rel._ref_GLU,'C',AMPARsyn[i])\n", " h.setpointer(Rel._ref_GLU,'C',NMDARsyn[i])\n", " \n", "####Running the Simulation####\n", " h.v_init=-85 #forced resting Vm for granule cells\n", " h.init()\n", "\n", " for l in range(nofsections):# dummy current source to compensate current caused by the forced Vm. \n", " gc[l].ic_constant=-(gc[l].ina+gc[l].ik+gc[l].ica)\n", " for l in range(nofspines): \n", " spineh[l].ic_constant=-(spineh[l].ina+spineh[l].ik+spineh[l].ica)\n", "\n", " if h.cvode.active():\n", " h.cvode.re_init()\n", " else:\n", " h.fcurrent()\n", " for i in range(nofspines): \n", " spineh[i].gcatbar_cathem=gcattype_vec[var]\n", "\n", " h.tstop =350\n", " h.run()\n", " \n", "#### Vectors and conversion of units (um to nm)####\n", " for i in range(nofspines):\n", " v_spineh[i]=np.asarray(vrec_spineh[i])\n", " ccaspineh_show[i]=1e6*np.asarray(ccaspineh[i])#converting to nM\n", " icahvacc_show[i]=np.asarray(icahvacc[i]) #mA/cm2\n", " icattype_show[i]=np.asarray(icattype[i]) #mA/cm2\n", "\n", " for i in range(nofsections):\n", " v_dend[i]=np.asarray(vrec_gc[i])\n", " ccagc_show[i]=1e6*np.asarray(ccagc[i])#converting to nM\n", "\n", "####Mapping of Ca Concentration to df/f####\n", " for i in range(nofspines): \n", " y_dff_spineh[i]=spine_fit(ccaspineh_show[i])\n", " \n", " for i in range(nofsections): \n", " y_dff_gc[i]=spine_fit(ccagc_show[i]) \n", " \n", " pickle.dump(v_spineh[0],vmspine_obj_ap)\n", " pickle.dump(ccaspineh_show[0],caspine_0_obj_ap)\n", " pickle.dump(y_dff_spineh[0],dffspine_0_obj_ap)\n", " pickle.dump(ccagc_show[11],cagc_obj_ap)\n", " pickle.dump(y_dff_gc[11],dffgc_obj_ap)\n", " \n", " pickle.dump(icattype_show[0],ittype_obj_ap)\n", " pickle.dump(icahvacc_show[0],ihvacc_obj_ap)\n", " \n", "caspine_0_obj_ap.close()\n", "dffspine_0_obj_ap.close()\n", "vmspine_obj_ap.close()\n", "cagc_obj_ap.close()\n", "dffgc_obj_ap.close()\n", "##\n", "ccabuf1spineh_obj_ap.close()\n", "ccabuf2spineh_obj_ap.close()\n", "cbuf1spineh_obj_ap.close()\n", "cbuf2spineh_obj_ap.close()\n", "##\n", "ittype_obj_ap.close()\n", "ihvacc_obj_ap.close()\n", "\n", "print \"run the next block\"" ], "language": "python", "metadata": {}, "outputs": [ { "ename": "KeyboardInterrupt", "evalue": "", "output_type": "pyerr", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)", "\u001b[0;32m<ipython-input-5-194e62291d66>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 237\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 238\u001b[0m \u001b[0mh\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtstop\u001b[0m \u001b[0;34m=\u001b[0m\u001b[0;36m350\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 239\u001b[0;31m \u001b[0mh\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 240\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 241\u001b[0m \u001b[0;31m#### Vectors and conversion of units (um to nm)####\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;31mKeyboardInterrupt\u001b[0m: " ] } ], "prompt_number": 5 }, { "cell_type": "code", "collapsed": false, "input": [ "####Coincidance Case-Glutamate and Global AP####\n", "\n", "import pickle\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", "from neuron import h,gui\n", "\n", "####Sections and Connections####\n", "nofsections = 27 # 1soma + 25dendritic sections + 1terminating section \n", "nofspines =1 # number of spines is 1 throughout this simulation\n", "\n", "gc=[h.Section() for i in range(nofsections)]\n", "spineh=[h.Section() for i in range(nofspines)]\n", "spinen=[h.Section() for i in range(nofspines)]\n", "\n", "for i in range(nofsections-1):\n", " gc[i+1].connect(gc[i],1,0)\n", "for i in range(nofspines):\n", " spineh[i].connect(spinen[i],0,1)\n", " \n", "j=0\n", "for i in range(nofspines): #spines start at 100um from soma, on 11th dendritic section\n", " spinen[i].connect(gc[11+j],0.5,1)\n", " j=j+1\n", " \n", "####Morphology and other Parameters#### \n", "h.celsius=22 #temperature\n", "h.dt=0.025 #temporal resolution,ms\n", "\n", "for i in range(nofsections): \n", " gc[i].L=10 #dendrite total length is 260 um\n", " gc[i].nseg=3\n", " gc[i].Ra=200\n", " \n", "gc[0].diam=10 #soma size is 10umx10um, and there are two tapering regimes:\n", "for i in range(1,11):#1.tapering starts at 2.35um, ends at 1.7um , first 10 sections as in Ona-Jodar et al. Front Cell Neurosci 2017 \n", " gc[i].diam=2.35-(i-1)*((2.35-1.7)/9)\n", "for i in range(11,27):#2.tapering starts at 1.7um ends at 1.2um, next 15 sections \n", " gc[i].diam=1.7-(i-10)*((1.7-1.2)/16)\n", " \n", "for i in range(nofspines): \n", " spineh[i].diam=1\n", " spinen[i].diam=0.3 \n", " spineh[i].L=1\n", " spinen[i].L=2.5\n", " spineh[i].nseg=3\n", " spinen[i].nseg=3\n", " spinen[i].Ra=4.9e3 #Ra is normalized as ohmcm.\n", " \n", "presyn=h.Section() #with all other default specifications\n", "presyn.L=10\n", "presyn.diam=10\n", "\n", "####Settings for Ion channels and Synaptic Receptors and their Parameters#### \n", "for i in range(nofsections):\n", " gc[i].insert('constant')#dummy current source\n", " gc[i].insert('cadifusnpumpOGBenddif')#ca and buffers diffusion,ca pumps \n", " gc[i].insert('nax')\n", " gc[i].insert('kamt')\n", " gc[i].insert('pas')\n", " gc[i].g_pas=6e-4 \n", " gc[i].e_pas=-85\n", " gc[i].gbar_nax=0.5\n", " gc[i].gbar_kamt=0.01\n", " gc[i].cm=1\n", " \n", " gc[i].insert('canhem')#HVA Ca2+ channel \n", " gc[i].insert('cathem')#T-type Ca2+ channel\n", " gc[i].q10_cathem=3\n", " gc[i].q10_canhem=3 \n", " gc[i].a0m_cathem=0.055633 #to adjust the opening rate\n", " gc[i].a0m_canhem=0.331432 #to adjust the opening rate \n", " gc[i].gcanbar_canhem=0.0005\n", " gc[i].gcatbar_cathem=0.0003\n", " \n", " gc[i].TotalPump_cadifusnpumpOGBenddif=2e-11 \n", " \n", "for i in range(nofspines): \n", " spineh[i].insert('constant')#dummy current source\n", " spineh[i].insert('cadifusnpumpOGBenddif')#ca and buffers diffusion,ca pumps \n", " spineh[i].insert('nax')\n", " spineh[i].insert('kamt')\n", " spineh[i].insert('pas')\n", " spineh[i].gbar_nax=0.5 #for pharmacology in-silico,No Nav Channel case,set it to 0 \n", " spineh[i].gbar_kamt=0.01\n", " spineh[i].g_pas=2e-4\n", " spineh[i].e_pas=-85\n", " spineh[i].cm=1\n", "\n", " spineh[i].insert('canhem')\n", " spineh[i].insert('cathem')\n", " spineh[i].q10_canhem=3\n", " spineh[i].q10_cathem=3\n", " spineh[i].a0m_cathem=0.055633 #to adjust the opening rate\n", " spineh[i].a0m_canhem=0.331432 #to adjust the opening rate\n", " \n", " spineh[i].gcanbar_canhem=0.0004 \n", "\n", " spineh[i].TotalPump_cadifusnpumpOGBenddif=2.2e-11 \n", " \n", "AMPARsyn=[h.AMPA5() for i in range(nofspines)]\n", "NMDARsyn=[h.NMDA5() for i in range(nofspines)]\n", "\n", "for i in range(nofspines): \n", " AMPARsyn[i].loc(spineh[i](0.3))\n", " AMPARsyn[i].gmax=2000\n", " NMDARsyn[i].loc(spineh[i](0.7))\n", " NMDARsyn[i].gmax=383 \n", " NMDARsyn[i].gmax_ca=17\n", " ##NMDAR Setting##\n", " NMDARsyn[i].Rb= 5e-3\n", " NMDARsyn[i].Ru=12.9e-3\n", " NMDARsyn[i].Rd=8.4e-3\n", " NMDARsyn[i].Rr=6.8e-3\n", " NMDARsyn[i].Ro=46.5e-3\n", " NMDARsyn[i].Rc=73.8e-3 \n", " ####\n", " spinen[i].insert('cadifusnpumpOGBenddif')\n", " spinen[i].TotalPump_cadifusnpumpOGBenddif=0 #there is no active mechanism on the neck\n", "\n", "####Setting Ca Dynamic Global Parameters####\n", "h.DCa_cadifusnpumpOGBenddif=0.6\n", "h.mg_NMDA5=1\n", "##endogenous buffer\n", "for i in range(nofsections):\n", " gc[i].k1buf1_cadifusnpumpOGBenddif=1000\n", " gc[i].k2buf1_cadifusnpumpOGBenddif=1\n", " gc[i].TotalBuffer1_cadifusnpumpOGBenddif=0.12\n", "for i in range(nofspines):\n", " spineh[i].k1buf1_cadifusnpumpOGBenddif=1000\n", " spineh[i].k2buf1_cadifusnpumpOGBenddif=1\n", " spineh[i].TotalBuffer1_cadifusnpumpOGBenddif=0.12\n", "##exogenous buffer \n", "for i in range(nofsections):\n", " gc[i].k1buf2_cadifusnpumpOGBenddif=1000\n", " gc[i].k2buf2_cadifusnpumpOGBenddif=0.2\n", " gc[i].TotalBuffer2_cadifusnpumpOGBenddif=0.1 #for \"no OGB case\", set this to 0\n", "for i in range(nofspines):\n", " spineh[i].k1buf2_cadifusnpumpOGBenddif=1000\n", " spineh[i].k2buf2_cadifusnpumpOGBenddif=0.2\n", " spineh[i].TotalBuffer2_cadifusnpumpOGBenddif=0.1 #for \"no OGB case\", set this to 0\n", "\n", "####Mapping of Ca Concentration to fluorescence signal df/f \u2013 based on experimental data and simulations, see Figure 3C; not valid for \"no OGB case\"####\n", "def spine_fit(x):\n", " y = 14390070 + (-49.1502 - 14390070)/(1 + (x/6632796000)**0.6715641)\n", " return y\n", " \n", "def dend_fit(x): #not calculated and used based on experiment\n", " y = 14390070 + (-49.1502 - 14390070)/(1 + (x/6632796000)**0.6715641)\n", " return y\n", "\n", "####Simulation Readout####\n", "time_h = h.Vector()\n", "time_h.record(h._ref_t)\n", "vrec_gc=[h.Vector() for i in range(nofsections)] #gc[0] is the soma, gc[10] is the 1th parent dendrite\n", "vrec_spineh=[h.Vector() for i in range(nofspines)] \n", "icaspineh=[h.Vector() for i in range(nofspines)] #overall influx\n", "ccaspineh=[h.Vector() for i in range(nofspines)] #overall concentration\n", "icagc=[h.Vector() for i in range(nofsections)] #overall influx\n", "ccagc=[h.Vector() for i in range(nofsections)] #overall concentration\n", "\n", "icahvacc=[h.Vector() for i in range(nofspines)]\n", "icattype=[h.Vector() for i in range(nofspines)]\n", "\n", "for i in range(nofsections): \n", " vrec_gc[i].record(gc[i](0.5)._ref_v)\n", "for i in range(nofspines): \n", " vrec_spineh[i].record(spineh[i](0.5)._ref_v) \n", "\n", "for i in range(nofspines): \n", " icahvacc[i].record(spineh[i](0.5)._ref_ica_canhem)\n", " icattype[i].record(spineh[i](0.5)._ref_ica_cathem)\n", " \n", " icaspineh[i].record(spineh[i](0.5)._ref_ica)\n", " ccaspineh[i].record(spineh[i](0.5)._ref_caiav_cadifusnpumpOGBenddif)\n", " \n", "for i in range(nofsections):\n", " icagc[i].record(gc[i](0.5)._ref_ica)\n", " ccagc[i].record(gc[i](0.5)._ref_caiav_cadifusnpumpOGBenddif) \n", " \n", "icattype_show=[np.array for i in range(nofspines)]\n", "icahvacc_show=[np.array for i in range(nofspines)]\n", "ccaspineh_show=[np.array for i in range(nofspines)]\n", "icaspineh_show=[np.array for i in range(nofspines)]\n", "ccagc_show=[np.array for i in range(nofsections)]\n", "icagc_show=[np.array for i in range(nofsections)] \n", "\n", "icattype_show=[np.array for i in range(nofspines)]\n", "icahvacc_show=[np.array for i in range(nofspines)]\n", "y_dff_spineh=[np.array for i in range(nofspines)]\n", "y_dff_gc=[np.array for i in range(nofsections)]\n", "v_dend=[np.array for i in range(nofsections)]\n", "v_spineh=[np.array for i in range(nofspines)]\n", "\n", "vmspine_obj=open(\"vmspine_0_record\",\"w\")\n", "caspine_0_obj=open(\"caspine_0_record\",\"w\")\n", "dffspine_0_obj=open(\"dffspine_0_record\",\"w\")\n", "cagc_obj=open(\"cagc\",\"w\")\n", "dffgc_obj=open(\"dffgc\",\"w\") \n", "ittype_obj=open(\"ittype\",\"w\")\n", "ihvacc_obj=open(\"ihvacc\",\"w\")\n", "\n", "t_c=[-100,-80,-60,-40,-20,-12,-10,-8,-7,-6,-5,-4,-3,-2,0,2,3,4,5,6,7,8,10,12,20,40,60,80,100]\n", "for tc in t_c:\n", " for var in range(30):\n", "####Setting Stimulation####\n", "#Current Clamp (Global AP)\n", " APstim1=h.IClamp(0.5,sec=gc[0])\n", " APstim1.delay=120+tc #mS\n", " APstim1.dur=3 #mS\n", " APstim1.amp=1 #nA\n", "#Glutamate \n", " Rel=h.STEP_REL(0.75,presyn)\n", " Rel.amplitude=1\n", " Rel.duration=3\n", " Rel.release_time=120\n", "\n", " for i in range(nofspines):\n", " h.setpointer(Rel._ref_GLU,'C',AMPARsyn[i])\n", " h.setpointer(Rel._ref_GLU,'C',NMDARsyn[i])\n", " \n", "####Running the Simulation####\n", " h.v_init=-85 #forced resting Vm for granule cells\n", " h.init()\n", "\n", " for l in range(nofsections):# dummy current source to compensate current caused by the forced Vm. \n", " gc[l].ic_constant=-(gc[l].ina+gc[l].ik+gc[l].ica)\n", " for l in range(nofspines): \n", " spineh[l].ic_constant=-(spineh[l].ina+spineh[l].ik+spineh[l].ica)\n", "\n", " if h.cvode.active():\n", " h.cvode.re_init()\n", " else:\n", " h.fcurrent()\n", " \n", " for i in range(nofspines): \n", " spineh[i].gcatbar_cathem=gcattype_vec[var] \n", "\n", " h.tstop =350\n", " h.run()\n", " \n", "#### Vectors and conversion of units (um to nm)####\n", " for i in range(nofspines):\n", " v_spineh[i]=np.asarray(vrec_spineh[i])\n", " ccaspineh_show[i]=1e6*np.asarray(ccaspineh[i])#converting to nM\n", " icahvacc_show[i]=np.asarray(icahvacc[i]) #mA/cm2\n", " icattype_show[i]=np.asarray(icattype[i]) #mA/cm2\n", " \n", " for i in range(nofsections):\n", " v_dend[i]=np.asarray(vrec_gc[i])\n", " ccagc_show[i]=1e6*np.asarray(ccagc[i])#converting to nM\n", "\n", "####Mapping of Ca Concentration to df/f####\n", " for i in range(nofspines): \n", " y_dff_spineh[i]=spine_fit(ccaspineh_show[i])\n", " \n", " for i in range(nofsections): \n", " y_dff_gc[i]=spine_fit(ccagc_show[i]) \n", " \n", " pickle.dump(v_spineh[0],vmspine_obj)\n", " pickle.dump(ccaspineh_show[0],caspine_0_obj)\n", " pickle.dump(y_dff_spineh[0],dffspine_0_obj)\n", " pickle.dump(ccagc_show[11],cagc_obj)\n", " pickle.dump(y_dff_gc[11],dffgc_obj)\n", "\n", " pickle.dump(icattype_show[0],ittype_obj)\n", " pickle.dump(icahvacc_show[0],ihvacc_obj)\n", " \n", "caspine_0_obj.close()\n", "dffspine_0_obj.close()\n", "vmspine_obj.close()\n", "cagc_obj.close()\n", "dffgc_obj.close()\n", "\n", "ittype_obj.close()\n", "ihvacc_obj.close()\n", "\n", "print \"run the next block\"" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "####Retrieving the Simulation Data###\n", "####only the recorded variables which are used for SE are retrieving here.\n", "##cases for normalization\n", "t_c2=t_c=[-100,-80,-60,-40,-20,-12,-10,-8,-7,-6,-5,-4,-3,-2,0,2,3,4,5,6,7,8,10,12,20,40,60,80,100]\n", "t_c1=[0]\n", "\n", "y_dff_spineh_apalone=[np.array for i in range(len(t_c2))]\n", "y_dff_spineh_glualone=[np.array for i in range(len(t_c1))]\n", "cca_apalone=[np.array for i in range(len(t_c2))]\n", "cca_glualone=[np.array for i in range(len(t_c1))]\n", "vm_apalone=[np.array for i in range(len(t_c2))]\n", "vm_glualone=[np.array for i in range(len(t_c1))]\n", "\n", "dff_obj_glu=open(\"dffspine_0_record_glu\",\"r\")\n", "dff_obj_ap=open(\"dffspine_0_record_ap\",\"r\")\n", "cca_obj_glu=open(\"caspine_0_record_glu\",\"r\")\n", "cca_obj_ap=open(\"caspine_0_record_ap\",\"r\")\n", "vm_obj_ap=open(\"vmspine_0_record_ap\",\"r\")\n", "vm_obj_glu=open(\"vmspine_0_record_glu\",\"r\")\n", "\n", "for tc in range(len(t_c2)):\n", " y_dff_spineh_apalone[tc]=pickle.load(dff_obj_ap)\n", " cca_apalone[tc]=pickle.load(cca_obj_ap)\n", " vm_apalone[tc]=pickle.load(vm_obj_ap)\n", " \n", "for tc in range(len(t_c1)):\n", " y_dff_spineh_glualone[tc]=pickle.load(dff_obj_glu)\n", " cca_glualone[tc]=pickle.load(cca_obj_glu)\n", " vm_glualone[tc]=pickle.load(vm_obj_glu) \n", "\n", "dff_obj_glu.close()\n", "dff_obj_ap.close()\n", "cca_obj_ap.close()\n", "cca_obj_glu.close()\n", "vm_obj_glu.close()\n", "vm_obj_ap.close()\n", "\n", "##cases for coincidance\n", "ccaspineh_av_l=[np.array for i in range(len(t_c))]\n", "y_dff_spineh_av_l=[np.array for i in range(len(t_c))]\n", "vm_l=[np.array for i in range(len(t_c))]\n", "\n", "vm_obj=open(\"vmspine_0_record\",\"r\")\n", "caspine_0_obj=open(\"caspine_0_record\",\"r\")\n", "dffspine_0_obj=open(\"dffspine_0_record\",\"r\")\n", "\n", "for tc in range(len(t_c)):\n", " ccaspineh_av_l[tc]=pickle.load(caspine_0_obj)\n", " y_dff_spineh_av_l[tc]=pickle.load(dffspine_0_obj)\n", " vm_l[tc]=pickle.load(vm_obj)\n", "\n", "caspine_0_obj.close()\n", "dffspine_0_obj.close()\n", "vm_obj.close()\n", "\n", "####Calculating SE####\n", "\n", "dff_add=[np.array for i in range(len(t_c))]\n", "cca_add=[np.array for i in range(len(t_c))]\n", "\n", "ext_ind_dff_add=[int for i in range(len(t_c))]\n", "ext_dff_add=[float for i in range(len(t_c))]\n", "\n", "ext_ind_cca_add=[int for i in range(len(t_c))]\n", "ext_cca_add=[float for i in range(len(t_c))]\n", "\n", "ext_ind_dff=[int for tc in range(len(t_c))]\n", "ext_dff=np.array([float for tc in range(len(t_c))])\n", "\n", "ext_ind_cca=[int for tc in range(len(t_c))]\n", "ext_cca=np.array([float for tc in range(len(t_c))])\n", "\n", "norm_cc=[float for i in range(len(t_c))]\n", "norm_dff=[float for i in range(len(t_c))]\n", "\n", "for tc in range(len(t_c)):\n", "\n", " dff_add[tc]=y_dff_spineh_apalone[tc]+y_dff_spineh_glualone[0]\n", " cca_add[tc]=cca_apalone[tc]+cca_glualone[0]-50\n", "\n", "for tc in range(len(t_c)):\n", " ext_ind_dff_add[tc]=np.argmax(dff_add[tc])\n", " ext_dff_add[tc]=dff_add[tc][ext_ind_dff_add[tc]]\n", " \n", " ext_ind_dff[tc]=np.argmax(y_dff_spineh_av_l[tc])\n", " ext_dff[tc]=round(y_dff_spineh_av_l[tc][ext_ind_dff[tc]],3)\n", " \n", "for tc in range(len(t_c)):\n", " ext_ind_cca_add[tc]=np.argmax(cca_add[tc])\n", " ext_cca_add[tc]=cca_add[tc][ext_ind_cca_add[tc]]\n", " \n", " ext_ind_cca[tc]=np.argmax(ccaspineh_av_l[tc])\n", " ext_cca[tc]=round(ccaspineh_av_l[tc][ext_ind_cca[tc]],3)\n", "\n", "for tc in range(len(t_c)): \n", " norm_cc[tc]=round(ext_cca[tc]/ext_cca_add[tc],3)\n", " norm_dff[tc]=round(ext_dff[tc]/ext_dff_add[tc],3)\n", " \n", "####Sample Plot####\n", "plt.suptitle('norm',fontsize=14)\n", "plt.plot(t_c,norm_dff,'go')\n", "plt.grid()\n", "plt.show()\n", "\n", "print 'ext_dff=',ext_dff\n", "print 'norm_dff=',norm_dff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "ext_dff= [64.533 65.295 65.938 65.756 61.584 56.311 54.302 51.753 50.13 48.035\n", " 38.531 35.885 36.972 38.327 41.211 43.005 44.1 46.573 50.403 54.694 58.321\n", " 61.096 65.234 68.378 76.271 81.193 80.246 78.278 76.106]\n", "norm_dff= [1.001, 0.998, 0.992, 0.972, 0.893, 0.81, 0.779, 0.741, 0.717, 0.687, 0.55, 0.512, 0.527, 0.546, 0.586, 0.611, 0.626, 0.66, 0.714, 0.775, 0.825, 0.864, 0.922, 0.966, 1.075, 1.146, 1.141, 1.126, 1.112]\n" ] } ], "prompt_number": 11 }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] } ], "metadata": {} } ] }
