{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "efa13610",
   "metadata": {},
   "outputs": [],
   "source": [
    "## Importing Neuron \n",
    "\n",
    "from neuron import h ,gui\n",
    "h.load_file(\"stdrun.hoc\")\n",
    "\n",
    "from Classes_Primary import Hu, Optrode, Sim\n",
    "cell = Hu()\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8b0ed1a4",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Soma photostimulation,  Fig 1C   \n",
    "# Run this cell --> load \"Primary_Photostim_Soma.ses\" --> init and run\n",
    "# for focal light -->  in \"Classes_primary.py\", uncomment line 577  and comment line 576\n",
    "\n",
    "optrode1 = Optrode(h.soma[1]) \n",
    "     "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1e4b017c",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Distal Axon photostimulation,  Fig 1C\n",
    "# Run this cell --> load \"Primary_Photostim_Distal_Axon.ses\" --> init and run\n",
    "\n",
    "\n",
    "optrode1 = Optrode(h.STIN[10]) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "adc68c1e",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Proximal Axon photostimulation,  Fig S4 panel C \n",
    "# Run this cell --> load \"Primary_Photostim_Proximal_Axon.ses\" --> init and run\n",
    "# scattered light --> in \"Classes_primary.py\", uncomment line 576  and comment line 577\n",
    "\n",
    "optrode1 = Optrode(h.STIN[7]) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f5fe54c1",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Fig 3.A,  Sample Traces\n",
    "# Run this cell --> load \"Fig3A.ses\" --> init and run\n",
    "\n",
    "\n",
    "p=0.95\n",
    "\n",
    "for i in range(0,17):\n",
    "    h.node[i].gbar_Kv1=h.node[i].gbar_Kv1- (p*h.node[i].gbar_Kv1)\n",
    "    \n",
    "for i in range(0,33):\n",
    "    h.MYSA[i].gbar_Kv1=h.MYSA[i].gbar_Kv1- (p*h.MYSA[i].gbar_Kv1)\n",
    "    \n",
    "for i in range(0,33):\n",
    "    h.FLUT[i].gbar_Kv1=h.FLUT[i].gbar_Kv1- (p*h.FLUT[i].gbar_Kv1)\n",
    "    \n",
    "for i in range(0,17):\n",
    "    h.STIN[i].gbar_Kv1=h.STIN[i].gbar_Kv1- (p*h.STIN[i].gbar_Kv1)\n",
    "    \n",
    "\n",
    "\n",
    "\n",
    "optrode1 = Optrode(h.STIN[8]) \n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "591c2dd5",
   "metadata": {},
   "outputs": [],
   "source": [
    "#Fig 2F, v  \n",
    "\n",
    "# Run this cell --> load \"Fig2F.ses\" --> init and run\n",
    "\n",
    "\n",
    "for i in range(0,30):\n",
    "    h.apical_dendrite[i].gbar_na3= h.apical_dendrite[i].gbar_na3-0.6* h.apical_dendrite[i].gbar_na3\n",
    "    \n",
    "for i in range(0,37):\n",
    "    h.user5[i].gbar_na3=h.user5[i].gbar_na3-0.6*h.user5[i].gbar_na3\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "h.soma[0].gbar_na3=h.soma[0].gbar_na3-0.9*h.soma[0].gbar_na3\n",
    "h.soma[1].gbar_na3=h.soma[1].gbar_na3-0.9*h.soma[1].gbar_na3 \n",
    "\n",
    "\n",
    "h.hill[0].gbar_na3=h.hill[0].gbar_na3-0.8*h.hill[0].gbar_na3\n",
    "h.user5[0].gbar_na3=h.user5[0].gbar_na3-0.8*h.user5[0].gbar_na3\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "h.ais[0].gbar_nax=h.ais[0].gbar_nax-0.7*h.ais[0].gbar_nax\n",
    "h.user5[1].gbar_na3=h.user5[1].gbar_na3-0.7*h.user5[1].gbar_na3\n",
    "h.user5[2].gbar_na3=h.user5[2].gbar_na3-0.7*h.user5[2].gbar_na3\n",
    "h.user5[3].gbar_na3=h.user5[3].gbar_na3-0.7*h.user5[3].gbar_na3\n",
    "h.apical_dendrite[26].gbar_na3=h.apical_dendrite[26].gbar_na3-0.7*h.apical_dendrite[26].gbar_na3\n",
    "h.apical_dendrite[27].gbar_na3=h.apical_dendrite[27].gbar_na3-0.7*h.apical_dendrite[27].gbar_na3\n",
    "h.apical_dendrite[22].gbar_na3=h.apical_dendrite[22].gbar_na3-0.7*h.apical_dendrite[22].gbar_na3\n",
    "h.apical_dendrite[29].gbar_na3=h.apical_dendrite[29].gbar_na3-0.7*h.apical_dendrite[29].gbar_na3\n",
    "h.apical_dendrite[23].gbar_na3=h.apical_dendrite[23].gbar_na3-0.7*h.apical_dendrite[23].gbar_na3\n",
    "h.apical_dendrite[22].gbar_na3=h.apical_dendrite[22].gbar_na3-0.7*h.apical_dendrite[22].gbar_na3\n",
    "h.apical_dendrite[30].gbar_na3=h.apical_dendrite[30].gbar_na3-0.7*h.apical_dendrite[30].gbar_na3\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "optrode1 = Optrode(h.STIN[8])\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "40697b2f",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Fig2H.  90% block of Na channels in the Axon   \n",
    "# Run this cell --> load \"Fig2H.ses\" --> init and run\n",
    "\n",
    "for i in range(0,17):\n",
    "    h.node[i].gbar_nax= h.node[i].gbar_nax-0.9* h.node[i].gbar_nax\n",
    "    h.STIN[i].gbar_nax= h.STIN[i].gbar_nax-0.9* h.STIN[i].gbar_nax\n",
    "\n",
    "\n",
    "for i in range(0,33):\n",
    "    h.MYSA[i].gbar_nax= h.MYSA[i].gbar_nax-0.9* h.MYSA[i].gbar_nax\n",
    "    h.FLUT[i].gbar_nax= h.FLUT[i].gbar_nax-0.9* h.FLUT[i].gbar_nax\n",
    "\n",
    "    \n",
    "optrode1 = Optrode(h.STIN[8])  "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e8bb44ca",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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