{ "cells": [ { "cell_type": "code", "execution_count": null, "id": "d7e45717", "metadata": {}, "outputs": [], "source": [ "from neuron import h\n", "import netpyne \n", "from netpyne import specs, sim \n", "import matplotlib.pyplot as plt\n", "import numpy as np\n", "from typing import Tuple, List\n", "\n", "import sys\n", "\n", "\n", "%matplotlib inline\n", "\n", "\n", "\n", "\n" ] }, { "cell_type": "code", "execution_count": null, "id": "7e8c705d", "metadata": {}, "outputs": [], "source": [ "# uniform diameter = 5.7\n", "\n", "\n", "# X=[37.7456209825333,\n", "# 32.1377001508427,\n", "# 34.0789035156587,\n", "# 28.4709826839680,\n", "# 39.6868243473493,\n", "# 30.4121860487840,\n", "# 36.0201068804747,\n", "# 24.8042652170933,\n", "# 26.5297793191520,\n", "# 22.8630618522773,\n", "# 35.8044176177173,\n", "# 30.1964967860267,\n", "# 43.3535418142240,\n", "# 41.4123384494080,\n", "# 41.6280277121653,\n", "# 32.3533894136000,\n", "# 45.2947451790400,\n", "# 26.7454685819093,\n", "# 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"70.8316177147634,\n", "85.1145365132137,\n", "78.2645652527324,\n", "41.6099318056892,\n", "83.0012475073205,\n", "81.1065746054853,\n", "85.8432568600734,\n", "76.4427643855832,\n", "66.7507837723491,\n", "15.6674874574837,\n", "1.82180086714926,\n", "31.4807189843393,\n", "8.08879585014273,\n", "60.9938930321574,\n", "36.5088893776712,\n", "21.8616104057912,\n", "53.7795615982463,\n", "70.9044897494494,\n", "78.1188211833605,\n", "45.5450216787316,\n", "84.0943280276101,\n", "7.14145939922511,\n", "9.40049247449020,\n", "26.8169087644372,\n", "0.0728720346859706,\n", "39.6423868691680,\n", "85.6246407560154,\n", "52.3221209045269,\n", "91.8916357390089,\n", "90.3613230106035,\n", "33.5211359555465,\n", "91.3815314962071,\n", "90.4341950452895,\n", "68.3539685354404,\n", "78.0459491486745,\n", "60.3380447199837,\n", "81.8352949523450,\n", "87.8836738312805,\n", "84.8230483744698,\n", "45.1077894706158,\n", "15.0116391453099,\n", "77.0257406630709,\n", "7.79730771139885,\n", "3.13349749149673,\n", "93.7134366061582,\n", "36.3631453082993,\n", "19.6025773305261,\n", "29.9504062559339,\n", "93.7134366061582,\n", "75.4225558999796,\n", "67.1880159804649,\n", "56.5486989163132,\n", "50.2817039333197,\n", "84.0214559929241,\n", "23.6105392382545,\n", "92.1831238777528,\n", "98.7416069994901,\n", "98.5958629301182,\n", "97.6485264792006,\n", "41.2455716322593,\n", "62.1598455871329,\n", "75.9326601427814,\n", "98.6687349648042,\n", "73.3821389287724,\n", "91.3086594615212,\n", "83.6570958194942,\n", "31.4807189843393,\n", "82.1267830910889,\n", "12.6797340353589,\n", "68.3539685354404,\n", "8.52602805825855,\n", "100.053303623838,\n", "95.3894934039355,\n", "23.9748994116843,\n", "0.947336450917617,\n", "18.3637527408646,\n", "91.5272755655791,\n", "97.2112942710848,\n", "78.3374372874184,\n", "88.5395221434543,\n", "2.91488138743882,\n", "99.9075595544657,\n", "89.4868585943719,\n", "99.0330951382340,\n", "3.86221783835644,\n", "95.7538535773653,\n", "84.6044322704119,\n", "12.0967577578711,\n", "97.5756544445146,\n", "90.8714272534053]\n", "\n", "C=[4.20000000000000,\n", "3,\n", "3.50000000000000,\n", "3,\n", "4.35000000000000,\n", "4.50000000000000,\n", "3.80000000000000,\n", "4.20000000000000,\n", "4.50000000000000,\n", "4.20000000000000,\n", "3.80000000000000,\n", "3.50000000000000,\n", "3.80000000000000,\n", "3.50000000000000,\n", "3.50000000000000,\n", "3.50000000000000,\n", "3.65000000000000,\n", "3.65000000000000,\n", "4.50000000000000,\n", "2.85000000000000,\n", "3.50000000000000,\n", "3.80000000000000,\n", "3.65000000000000,\n", "3,\n", "3.80000000000000,\n", "4.35000000000000,\n", "2.70000000000000,\n", "3.50000000000000,\n", "2.70000000000000,\n", "3.80000000000000,\n", "3.65000000000000,\n", "4.20000000000000,\n", "3,\n", "3.80000000000000,\n", "3.65000000000000,\n", "4.35000000000000,\n", "3.80000000000000,\n", "3.50000000000000,\n", "3.50000000000000,\n", "3,\n", "4.50000000000000,\n", "3,\n", "2.85000000000000,\n", "3.50000000000000,\n", "4.20000000000000,\n", "4.20000000000000,\n", "4.20000000000000,\n", "2.70000000000000,\n", "3.50000000000000,\n", "4.50000000000000,\n", "3,\n", "3.80000000000000,\n", "3,\n", "2.85000000000000,\n", "3.50000000000000,\n", "4.35000000000000,\n", "4.50000000000000,\n", "4.35000000000000,\n", "2.70000000000000,\n", "3.50000000000000,\n", "3,\n", "3,\n", "4.50000000000000,\n", "3.65000000000000,\n", "4.20000000000000,\n", "4.35000000000000,\n", "2.85000000000000,\n", "4.50000000000000,\n", "2.70000000000000,\n", "4.20000000000000,\n", "4.20000000000000,\n", "4.20000000000000,\n", "2.85000000000000,\n", "3.65000000000000,\n", "3.65000000000000,\n", "3.65000000000000,\n", "4.35000000000000,\n", "4.20000000000000,\n", "4.35000000000000,\n", "3.65000000000000,\n", "4.50000000000000,\n", "2.70000000000000,\n", "3.65000000000000,\n", "3,\n", "3.65000000000000,\n", "4.20000000000000,\n", "2.85000000000000,\n", "3.80000000000000,\n", "3,\n", "4.35000000000000,\n", "2.85000000000000,\n", "2.70000000000000,\n", "4.50000000000000,\n", "2.85000000000000,\n", "2.85000000000000,\n", "2.85000000000000,\n", "2.70000000000000,\n", "3.65000000000000,\n", "4.20000000000000,\n", "4.35000000000000,\n", "4.35000000000000,\n", "4.20000000000000,\n", "3.65000000000000,\n", "4.20000000000000,\n", "4.50000000000000,\n", "3.65000000000000,\n", "3,\n", "4.35000000000000,\n", "3,\n", "3,\n", "3.65000000000000,\n", "3.80000000000000,\n", "3.80000000000000,\n", "2.85000000000000,\n", "2.85000000000000,\n", "3,\n", "4.20000000000000,\n", "3.50000000000000,\n", "4.35000000000000,\n", "4.50000000000000,\n", "3.50000000000000,\n", "2.70000000000000,\n", "3.80000000000000,\n", "4.20000000000000,\n", "3,\n", "3.65000000000000,\n", "2.85000000000000,\n", "4.50000000000000,\n", "3.65000000000000,\n", "3.65000000000000,\n", "2.85000000000000,\n", "2.70000000000000,\n", "2.70000000000000,\n", "4.35000000000000,\n", "4.20000000000000,\n", "2.85000000000000,\n", "4.50000000000000,\n", "4.20000000000000,\n", "3.80000000000000,\n", "4.50000000000000,\n", "2.70000000000000,\n", "3.50000000000000,\n", "3.65000000000000,\n", "3.80000000000000,\n", "2.70000000000000,\n", "3.80000000000000,\n", "2.70000000000000,\n", "3.80000000000000,\n", "4.20000000000000,\n", "3.65000000000000,\n", "3.80000000000000,\n", "2.85000000000000,\n", "3.80000000000000,\n", "3.50000000000000,\n", "2.70000000000000,\n", "3.50000000000000,\n", "3,\n", "3,\n", "3.80000000000000,\n", "3.65000000000000,\n", "3.50000000000000,\n", "2.85000000000000,\n", "4.35000000000000,\n", "4.35000000000000,\n", "3,\n", "3.80000000000000,\n", "4.35000000000000,\n", "4.50000000000000,\n", "4.50000000000000,\n", "3.50000000000000,\n", "2.85000000000000,\n", "4.35000000000000,\n", "2.85000000000000,\n", "2.85000000000000,\n", "3.50000000000000,\n", "4.35000000000000,\n", "3.80000000000000,\n", "3.80000000000000,\n", "4.50000000000000,\n", "3.80000000000000,\n", "2.70000000000000,\n", "4.35000000000000,\n", "3.80000000000000,\n", "3.65000000000000,\n", "3,\n", "3,\n", "3.65000000000000,\n", "3,\n", "2.70000000000000,\n", "2.85000000000000,\n", "3,\n", "2.85000000000000,\n", "3.80000000000000,\n", "4.35000000000000,\n", "4.35000000000000,\n", "4.35000000000000,\n", "4.20000000000000,\n", "4.35000000000000,\n", "4.35000000000000,\n", "2.85000000000000]" ] }, { "cell_type": "code", "execution_count": null, "id": "be70ed3c", "metadata": {}, "outputs": [], "source": [ "# Network parameters\n", "netParams = specs.NetParams()\n", "\n", "\n", "netParams.sizeX=3000\n", "netParams.sizeY=3000\n", "netParams.sizeZ=3000" ] }, { "cell_type": "code", "execution_count": null, "id": "99c70926", "metadata": {}, "outputs": [], "source": [ "netParams.importCellParams(\n", " cellInstance=True,\n", " label='MRGaxon5.7', \n", " conds={'cellType': 'MRGaxon5.7', 'cellModel': 'MRGaxon5.7'},\n", " fileName='MRGaxon5.7.hoc', \n", " cellName='MRGaxon5.7', \n", " importSynMechs=True) ;\n", "\n", "\n", "netParams.importCellParams(\n", " cellInstance=True,\n", " label='MRGaxon5.4', \n", " conds={'cellType': 'MRGaxon5.4', 'cellModel': 'MRGaxon5.4'},\n", " fileName='MRGaxon5.4.hoc', \n", " cellName='MRGaxon5.4', \n", " importSynMechs=True) ;\n", "\n", "\n", "\n", "netParams.importCellParams(\n", " cellInstance=True,\n", " label='MRGaxon6', \n", " conds={'cellType': 'MRGaxon6', 'cellModel': 'MRGaxon6'},\n", " fileName='MRGaxon6.hoc', \n", " cellName='MRGaxon6', \n", " importSynMechs=True) ;\n", "\n", "\n", "netParams.importCellParams(\n", " cellInstance=True,\n", " label='MRGaxon7.3', \n", " conds={'cellType': 'MRGaxon7.3', 'cellModel': 'MRGaxon7.3'},\n", " fileName='MRGaxon7.3.hoc', \n", " cellName='MRGaxon7.3', \n", " importSynMechs=True) ;\n", "\n", "\n", "\n", "\n", "netParams.importCellParams(\n", " cellInstance=True,\n", " label='MRGaxon8.7', \n", " conds={'cellType': 'MRGaxon8.7', 'cellModel': 'MRGaxon8.7'},\n", " fileName='MRGaxon8.7.hoc', \n", " cellName='MRGaxon8.7', \n", " importSynMechs=True) ;\n", "\n", "\n", "netParams.importCellParams(\n", " cellInstance=True,\n", " label='MRGaxon7', \n", " conds={'cellType': 'MRGaxon7', 'cellModel': 'MRGaxon7'},\n", " fileName='MRGaxon7.hoc', \n", " cellName='MRGaxon7', \n", " importSynMechs=True) ;\n", "\n", "\n", "\n", "netParams.importCellParams(\n", " cellInstance=True,\n", " label='MRGaxon7.6', \n", " conds={'cellType': 'MRGaxon7.6', 'cellModel': 'MRGaxon7.6'},\n", " fileName='MRGaxon7.6.hoc', \n", " cellName='MRGaxon7.6', \n", " importSynMechs=True) ;\n", "\n", "\n", "\n", "netParams.importCellParams(\n", " cellInstance=True,\n", " label='MRGaxon8.4', \n", " conds={'cellType': 'MRGaxon8.4', 'cellModel': 'MRGaxon8.4'},\n", " fileName='MRGaxon8.4.hoc', \n", " cellName='MRGaxon8.4', \n", " importSynMechs=True) ;\n", "\n", "\n", "netParams.importCellParams(\n", " cellInstance=True,\n", " label='MRGaxon9', \n", " conds={'cellType': 'MRGaxon9', 'cellModel': 'MRGaxon9'},\n", " fileName='MRGaxon9.hoc', \n", " cellName='MRGaxon9', \n", " importSynMechs=True) ;\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "#netParams.cellParams['MRGaxon5.7']['secs']['node_0']['spikeGenLoc'] = 0.5\n" ] }, { "cell_type": "code", "execution_count": null, "id": "a3473ceb", "metadata": {}, "outputs": [], "source": [ "#netParams.popParams['MRGaxon5.7'] = {'cellType': 'MRGaxon5.7', \n", "#\t'gridSpacing': 6, \n", "#\t'cellModel': 'MRGaxon5.7', \n", "#\t'xRange':[1, 85], \n", "#\t'yRange':[0, 0], \n", "#\t'zRange':[1, 85]} #[1, 85]\n", "\n", "\n", "\n", "\n", "\n", "\n", "for i in range(200):\n", " \n", " \n", " if C[i]==2.7:\n", " \n", " netParams.popParams[\"MRGaxon5.4_%s\" %i] = {'cellType': 'MRGaxon5.4', \n", "\t 'numCells':1 , #'gridSpacing': 6, \n", "\t 'cellModel': 'MRGaxon5.4', \n", "\t 'xRange':[X[i], X[i]], \n", "\t 'yRange':[0, 0], \n", " 'zRange':[Y[i], Y[i]]} \n", " \n", " if C[i]==2.85:\n", " \n", " netParams.popParams[\"MRGaxon5.7_%s\" %i] = {'cellType': 'MRGaxon5.7', \n", "\t 'numCells':1 , #'gridSpacing': 6, \n", "\t 'cellModel': 'MRGaxon5.7', \n", "\t 'xRange':[X[i], X[i]], \n", "\t 'yRange':[0, 0], \n", " 'zRange':[Y[i], Y[i]]} \n", " \n", " if C[i]==3:\n", " \n", " netParams.popParams[\"MRGaxon6_%s\" %i] = {'cellType': 'MRGaxon6', \n", "\t 'numCells':1 , #'gridSpacing': 6, \n", "\t 'cellModel': 'MRGaxon6', \n", "\t 'xRange':[X[i], X[i]], \n", "\t 'yRange':[0, 0], \n", " 'zRange':[Y[i], Y[i]]} \n", " \n", " \n", " if C[i]==3.5:\n", " \n", " netParams.popParams[\"MRGaxon7_%s\" %i] = {'cellType': 'MRGaxon7', \n", "\t 'numCells':1 , #'gridSpacing': 6, \n", "\t 'cellModel': 'MRGaxon7', \n", "\t 'xRange':[X[i], X[i]], \n", "\t 'yRange':[0, 0], \n", " 'zRange':[Y[i], Y[i]]} \n", " \n", " \n", " if C[i]==3.65:\n", " \n", " netParams.popParams[\"MRGaxon7.3_%s\" %i] = {'cellType': 'MRGaxon7.3', \n", "\t 'numCells':1 , #'gridSpacing': 6, \n", "\t 'cellModel': 'MRGaxon7.3', \n", "\t 'xRange':[X[i], X[i]], \n", "\t 'yRange':[0, 0], \n", " 'zRange':[Y[i], Y[i]]} \n", " \n", " \n", " if C[i]==3.8:\n", " \n", " netParams.popParams[\"MRGaxon7.6_%s\" %i] = {'cellType': 'MRGaxon7.6', \n", "\t 'numCells':1 , #'gridSpacing': 6, \n", "\t 'cellModel': 'MRGaxon7.6', \n", "\t 'xRange':[X[i], X[i]], \n", "\t 'yRange':[0, 0], \n", " 'zRange':[Y[i], Y[i]]} \n", " \n", " \n", " \n", " if C[i]==4.2:\n", " \n", " netParams.popParams[\"MRGaxon8.4_%s\" %i] = {'cellType': 'MRGaxon8.4', \n", "\t 'numCells':1 , #'gridSpacing': 6, \n", "\t 'cellModel': 'MRGaxon8.4', \n", "\t 'xRange':[X[i], X[i]], \n", "\t 'yRange':[0, 0], \n", " 'zRange':[Y[i], Y[i]]} \n", " \n", " \n", " \n", " \n", " if C[i]==4.35:\n", " \n", " netParams.popParams[\"MRGaxon8.7_%s\" %i] = {'cellType': 'MRGaxon8.7', \n", "\t 'numCells':1 , #'gridSpacing': 6, \n", "\t 'cellModel': 'MRGaxon8.7', \n", "\t 'xRange':[X[i], X[i]], \n", "\t 'yRange':[0, 0], \n", " 'zRange':[Y[i], Y[i]]} \n", " \n", " \n", " \n", " if C[i]==4.5:\n", " \n", " netParams.popParams[\"MRGaxon9_%s\" %i] = {'cellType': 'MRGaxon9', \n", "\t 'numCells':1 , #'gridSpacing': 6, \n", "\t 'cellModel': 'MRGaxon9', \n", "\t 'xRange':[X[i], X[i]], \n", "\t 'yRange':[0, 0], \n", " 'zRange':[Y[i], Y[i]]} \n", " \n", " \n", " \n", " \n", " \n", " \n", "#for i in range(62,124):\n", " \n", "\n", " #netParams.popParams[\"MRGaxon7.3_%s\" %i] = {'cellType': 'MRGaxon7.3', \n", "\t#'numCells':1 , #'gridSpacing': 6, \n", "\t#'cellModel': 'MRGaxon7.3', \n", "\t#'xRange':[X[i], X[i]], \n", "\t#'yRange':[0, 0], \n", " #'zRange':[Y[i], Y[i]]} \n", " \n", " \n", " \n", "#for i in range(62): #188\n", " \n", "\n", " #netParams.popParams[\"MRGaxon8.7_%s\" %i] = {'cellType': 'MRGaxon8.7', \n", "\t#'numCells':1 , #'gridSpacing': 6, \n", "\t#'cellModel': 'MRGaxon8.7', \n", "\t#'xRange':[X[i], X[i]], \n", "\t#'yRange':[0, 0], \n", " #'zRange':[Y[i], Y[i]]} \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "#netParams.popParams['MRGaxon7.3'] = {'cellType': 'MRGaxon7.3', \n", "#\t'numCells': 66, \n", "#\t'cellModel': 'MRGaxon7.3', \n", "#\t'xRange':[-0.1, 0.1], \n", "#\t'yRange':[-0.1, 0.1], \n", "#\t'zRange':[-0.1, 0.1]} \n", "\n", "\n", "#netParams.popParams['MRGaxon8.7'] = {'cellType': 'MRGaxon8.7', \n", "#\t'numCells': 66, \n", "#\t'cellModel': 'MRGaxon8.7', \n", "#\t'xRange':[-0.1, 0.1], \n", "#\t'yRange':[-0.1, 0.1], \n", "#\t'zRange':[-0.1, 0.1]} " ] }, { "cell_type": "code", "execution_count": null, "id": "5042eeb4", "metadata": {}, "outputs": [], "source": [ "netParams.stimSourceParams['Input_1'] = {'type': 'IClamp', 'del': 1, 'dur': 0.1, 'amp': 2}\n", "\n", "\n", "\n", "\n", "for i in range(200):\n", " if C[i]==2.7:\n", " netParams.stimTargetParams['Input_1->\"S1_%s\"' %i] = {'source': 'Input_1', 'sec':'node_0', 'loc': 0.5, 'conds': {'pop':\"MRGaxon5.4_%s\" %i}} # , 'cellList': [0,]\n", " \n", " if C[i]==2.85:\n", " netParams.stimTargetParams['Input_1->\"S2_%s\"' %i] = {'source': 'Input_1', 'sec':'node_0', 'loc': 0.5, 'conds': {'pop':\"MRGaxon5.7_%s\" %i}} # , 'cellList': [0,]\n", " \n", " if C[i]==3:\n", " netParams.stimTargetParams['Input_1->\"S3_%s\"' %i] = {'source': 'Input_1', 'sec':'node_0', 'loc': 0.5, 'conds': {'pop':\"MRGaxon6_%s\" %i}} # , 'cellList': [0,]\n", " \n", "# if C[i]==3.5:\n", "# netParams.stimTargetParams['Input_1->\"S4_%s\"' %i] = {'source': 'Input_1', 'sec':'node_0', 'loc': 0.5, 'conds': {'pop':\"MRGaxon7_%s\" %i}} # , 'cellList': [0,]\n", " \n", "# if C[i]==3.65: \n", "# netParams.stimTargetParams['Input_1->\"S5_%s\"' %i] = {'source': 'Input_1', 'sec':'node_0', 'loc': 0.5, 'conds': {'pop':\"MRGaxon7.3_%s\" %i}} # , 'cellList': [0,]\n", " \n", " \n", "# if C[i]==3.8:\n", "# netParams.stimTargetParams['Input_1->\"S6_%s\"' %i] = {'source': 'Input_1', 'sec':'node_0', 'loc': 0.5, 'conds': {'pop':\"MRGaxon7.6_%s\" %i}} # , 'cellList': [0,]\n", " \n", " \n", "# if C[i]==4.2:\n", "# netParams.stimTargetParams['Input_1->\"S7_%s\"' %i] = {'source': 'Input_1', 'sec':'node_0', 'loc': 0.5, 'conds': {'pop':\"MRGaxon8.4_%s\" %i}} # , 'cellList': [0,]\n", " \n", " \n", "# if C[i]==4.35:\n", "# netParams.stimTargetParams['Input_1->\"S8_%s\"' %i] = {'source': 'Input_1', 'sec':'node_0', 'loc': 0.5, 'conds': {'pop':\"MRGaxon8.7_%s\" %i}} # , 'cellList': [0,]\n", " \n", "# if C[i]==4.5:\n", "# netParams.stimTargetParams['Input_1->\"S9_%s\"' %i] = {'source': 'Input_1', 'sec':'node_0', 'loc': 0.5, 'conds': {'pop':\"MRGaxon9_%s\" %i}} # , 'cellList': [0,]\n", " \n", " \n", "#for i in range(62,124):\n", " #netParams.stimTargetParams['Input_1->\"SS_%s\"' %i] = {'source': 'Input_1', 'sec':'node_0', 'loc': 0.5, 'conds': {'pop':\"MRGaxon7.3_%s\" %i}} \n", " \n", "#for i in range(62):\n", " #netParams.stimTargetParams['Input_1->\"SSS_%s\"' %i] = {'source': 'Input_1', 'sec':'node_0', 'loc': 0.5, 'conds': {'pop':\"MRGaxon8.7_%s\" %i}} \n", " \n", " \n", " \n", "#netParams.stimTargetParams['Input_1->S'] = {'source': 'Input_1', 'sec':'node_0', 'loc': 0.5, 'conds': {'pop':'MRGaxon5.7'}}\n", "#netParams.stimTargetParams['Input_1->SS'] = {'source': 'Input_1', 'sec':'node_0', 'loc': 0.5, 'conds': {'pop':'MRGaxon7.3'}} \n", "#netParams.stimTargetParams['Input_1->SSS'] = {'source': 'Input_1', 'sec':'node_0', 'loc': 0.5, 'conds': {'pop':'MRGaxon8.7'}} " ] }, { "cell_type": "code", "execution_count": null, "id": "a7e41a19", "metadata": {}, "outputs": [], "source": [ "simConfig = specs.SimConfig()\n", "\n", "#simConfig.dt = 0.00001 # Internal integration timestep to use\n", "simConfig.duration = 3\n", "simConfig.recordStim = True\n", "simConfig.recordStep = 0.01 # Step size in ms to save data (e.g. V traces, LFP, etc)\n", "simConfig.hParams = {'celsius': 37 }\n", "#simConfig.cache_efficient = True\n", "simConfig.cvode_active = True\n", "simConfig.cvode_atol=0.0001\n", "simConfig.cvode_rtol=0.0001\n", "\n", "\n", "\n", "\n", "\n", "simConfig.recordTraces = {'V_node_7' :{'sec':'node_7','loc':0.5,'var':'v'}}\n", "simConfig.analysis['plotTraces'] = {'include': ['MRGaxon8.4_0','MRGaxon5.4_26']} #,('MRGaxon7.3',[0,60]),('MRGaxon8.7',[0,60])] , 'saveFig': True} \n", "#simConfig.analysis['plotTraces'] = {'include': ['MRGaxon7_0','MRGaxon6_1','MRGaxon7.6_2','MRGaxon5.7_23']}\n", "\n", "\n", "\n", "\n", "simConfig.recordLFP = [[56.39,-4000,51.74]] # ,[0,-4000,0],[-0.03,-8000,0],[0.03,-5000,0.02]]\n", "\n", "\n", "\n", "\n", "\n", "#simConfig.recordLFP = [[79.73,-4000,85]]\n", "#simConfig.analysis['plotLFP'] = True # showFig=True{'includeAxon': False, 'plots': ['timeSeries', 'locations'], 'figSize': (5,9), 'saveFig': True}\n", "#simConfig.recordLFP = [[0,-4000,0]]\n", "\n", "simConfig.analysis['plot2Dnet'] = True\n", "\n", "#simConfig.analysis['plot2Dnet'] = { 'include': ['allCells'], 'view'=xy }\n", "#simConfig.analysis['plot2Dnet'] = { 'include': ['allCells'], 'view':xy }\n", "#sim.initialize(netParams, simConfig)" ] }, { "cell_type": "code", "execution_count": null, "id": "ef4e29da", "metadata": {}, "outputs": [], "source": [ "#sim.createSimulateAnalyze(netParams, simConfig)\n", "\n", "sim.create(netParams, simConfig)" ] }, { "cell_type": "code", "execution_count": null, "id": "e8c5db2f", "metadata": { "scrolled": false }, "outputs": [], "source": [ "#netParams.cellParams['MRGaxon']['secs']" ] }, { "cell_type": "code", "execution_count": null, "id": "db1d59f7", "metadata": {}, "outputs": [], "source": [ "\n", "\n", "\n", "\n", "\n", "\n", "for j in range(200):\n", " \n", " \n", " S = sim.net.cells[j].secs[\"soma\"][\"hObj\"]\n", " for seg in S:\n", " seg.xraxial[0] = 5.8574e05\n", " seg.xraxial[1] = 1e09\n", " seg.xg[0] = 1e10\n", " seg.xg[1] = 1e09\n", " seg.xc[0] = 0\n", " seg.xc[1] = 0\n", "\n", "\n", "\n", "\n", "\n", "\n", " for i in range(21):\n", " S = sim.net.cells[j].secs[\"node_%s\" %i][\"hObj\"]\n", " for seg in S:\n", " seg.xraxial[0] = 5.8574e05\n", " seg.xraxial[1] = 1e09\n", " seg.xg[0] = 1e10\n", " seg.xg[1] = 1e09\n", " seg.xc[0] = 0\n", " seg.xc[1] = 0\n", "\n", "\n", " for i in range(40):\n", " S = sim.net.cells[j].secs[\"MYSA_%s\" %i][\"hObj\"]\n", " for seg in S:\n", " seg.xraxial[0] = 5.8574e05\n", " seg.xraxial[1] = 1e09\n", " seg.xg[0] = 6.25e-06\n", " seg.xg[1] = 1e09\n", " seg.xc[0] = 0.000625\n", " seg.xc[1] = 0\n", " \n", " \n", " for i in range(40):\n", " S = sim.net.cells[j].secs[\"FLUT_%s\" %i][\"hObj\"]\n", " for seg in S:\n", " seg.xraxial[0] = 1.6364e05\n", " seg.xraxial[1] = 1e09\n", " seg.xg[0] = 6.25e-06\n", " seg.xg[1] = 1e09\n", " seg.xc[0] = 0.000625\n", " seg.xc[1] = 0 \n", " \n", " \n", " for i in range(120):\n", " S = sim.net.cells[j].secs[\"STIN_%s\" %i][\"hObj\"]\n", " for seg in S:\n", " seg.xraxial[0] = 1.6364e05\n", " seg.xraxial[1] = 1e09\n", " seg.xg[0] = 6.25e-06\n", " seg.xg[1] = 1e09\n", " seg.xc[0] = 0.000625\n", " seg.xc[1] = 0\n", " \n", "\n", "\n", " \n", " " ] }, { "cell_type": "code", "execution_count": null, "id": "a634fff5", "metadata": {}, "outputs": [], "source": [ "sl = h.SectionList()\n", "\n", "N=h.Vector(2)\n", "\n", "for w in range(2):\n", " j=0\n", " NSEG=0\n", " \n", " for i in range(21):\n", " \n", " S = sim.net.cells[w].secs[\"node_%s\" %i][\"hObj\"]\n", " NSEG=NSEG+S.nseg\n", " sl.append(S)\n", " \n", " if j<39: \n", " S = sim.net.cells[w].secs[\"MYSA_%s\" %j][\"hObj\"]\n", " NSEG=NSEG+S.nseg\n", " sl.append(S)\n", " S = sim.net.cells[w].secs[\"FLUT_%s\" %j][\"hObj\"]\n", " NSEG=NSEG+S.nseg\n", " sl.append(S)\n", " \n", " if i<20:\n", " for k in range(i*6,i*6+6):\n", " S = sim.net.cells[w].secs[\"STIN_%s\" %k][\"hObj\"]\n", " NSEG=NSEG+S.nseg\n", " sl.append(S)\n", " \n", " if j<39: \n", " j=j+1\n", " S = sim.net.cells[w].secs[\"FLUT_%s\" %j][\"hObj\"]\n", " NSEG=NSEG+S.nseg\n", " sl.append(S)\n", " \n", " S = sim.net.cells[w].secs[\"MYSA_%s\" %j][\"hObj\"]\n", " NSEG=NSEG+S.nseg\n", " sl.append(S)\n", " \n", " j=j+1\n", " \n", " \n", " N[w]=NSEG\n", " \n", "\n", "\n", " \n", "nsegs=int(N[0])\n", " \n", " \n", "\n", "\n" ] }, { "cell_type": "code", "execution_count": null, "id": "9163f47c", "metadata": {}, "outputs": [], "source": [ "gmat =h.Matrix(2*nsegs, 2*nsegs, 2)\n", "cmat =h.Matrix(2*nsegs, 2*nsegs, 2)\n", "bvec =h.Vector(2*nsegs)\n", "xl =h.Vector(2*nsegs)\n", "layer =h.Vector(2*nsegs)\n", "layer.fill(2)\n", "\n", "e = h.Vector(2*nsegs)\n", "\n", " \n", " \n", "for i in range(2*nsegs): \n", " xl[i] = 0.5\n", "\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", "ge=1000\n", "\n", "for i in range(0,nsegs,1):\n", " gmat.setval(i, i, ge)\n", " gmat.setval(i, nsegs+i, -ge)\n", " gmat.setval(nsegs+i, i, -ge)\n", " gmat.setval(nsegs+i, nsegs+i, ge)\n", " \n", " \n", " \n", " \n", "lm = h.LinearMechanism(cmat, gmat, e, bvec, sl, xl, layer)" ] }, { "cell_type": "code", "execution_count": null, "id": "24e025bd", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "id": "adcad818", "metadata": { "scrolled": true }, "outputs": [], "source": [ "sim.simulate()\n", "#sim.h.CVode().atol(1e-6)\n", "sim.analyze()" ] }, { "cell_type": "code", "execution_count": null, "id": "21dee06e", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "id": "aab6e0c1", "metadata": { "scrolled": true }, "outputs": [], "source": [ "\n", "sim.analysis.plot2Dnet(include=['allCells'], view='xz' )\n", "\n", "\n", "#sim.analysis.plotLFP( plots = ['timeSeries', 'locations'] , electrodes=['avg', 'all'], lineWidth=100 , fontSize=14) \n", "\n", "#sim.analysis.plotLFP(include=['locations'])" ] }, { "cell_type": "code", "execution_count": null, "id": "433a88e6", "metadata": { "scrolled": false }, "outputs": [], "source": [ "np.set_printoptions(threshold=np.inf)\n", "#sim.analysis.plotShape(includePre=['all'],includePost=['all'],showElectrodes=True,dist=0.3, axis='[1]')\n", "sim.analysis.plotLFP( plots = ['timeSeries', 'locations'] , electrodes=[ 'all'], lineWidth=1000 , fontSize=14, saveFig=True) \n", "#sim.analysis.plotLFP(include=['locations'])\n" ] }, { "cell_type": "code", "execution_count": null, "id": "77d052c5", "metadata": {}, "outputs": [], "source": [ "#sim.analysis.plotShape(includePre=[], includePost=['MRGaxon'], showSyns=False, figSize=(4,9), dist=0.8, showFig=True)" ] }, { "cell_type": "code", "execution_count": null, "id": "45396b6f", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "id": "6c0d13e1", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "id": "6fbd9852", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "id": "9bbb366a", "metadata": {}, "outputs": [], "source": [ "#slist1.printnames()\n" ] }, { "cell_type": "code", "execution_count": null, "id": "727eca36", "metadata": {}, "outputs": [], "source": [ "\n", " \n", " \n" ] }, { "cell_type": "code", "execution_count": null, "id": "22f91a22", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "id": "9119afe0", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "id": "fbdf92a6", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "id": "8c1c6cb2", "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.8.8" } }, "nbformat": 4, "nbformat_minor": 5 }