cfg.py

"""
cfg.py 

Simulation configuration for M1 model (using NetPyNE)

Contributors: salvadordura@gmail.com
"""

from netpyne import specs
import pickle

cfg = specs.SimConfig()  

#------------------------------------------------------------------------------
#
# SIMULATION CONFIGURATION
#
#------------------------------------------------------------------------------

#------------------------------------------------------------------------------
# Run parameters
#------------------------------------------------------------------------------
cfg.duration = 6.0*1e3 
cfg.dt = 0.025
cfg.seeds = {'conn': 4321, 'stim': 1234, 'loc': 4321} 
cfg.hParams = {'celsius': 34, 'v_init': -80}  
cfg.verbose = 0
cfg.createNEURONObj = 1
cfg.createPyStruct = 1
cfg.connRandomSecFromList = False  # set to false for reproducibility 
cfg.cvode_active = False
cfg.cvode_atol = 1e-6
cfg.cache_efficient = True
cfg.printRunTime = 0.1

cfg.includeParamsLabel = False
cfg.printPopAvgRates = True

cfg.checkErrors = False


#------------------------------------------------------------------------------
# Recording 
#------------------------------------------------------------------------------
allpops = ['IT2','PV2','SOM2','IT4','IT5A','PV5A','SOM5A','IT5B','PT5B','PV5B','SOM5B','IT6','CT6','PV6','SOM6']
cfg.cellsrec = -1
if cfg.cellsrec == 0:  cfg.recordCells = ['all'] # record all cells
elif cfg.cellsrec == 1: cfg.recordCells = [(pop,50) for pop in allpops] # record one cell of each pop
elif cfg.cellsrec == 2: cfg.recordCells = [4073]
elif cfg.cellsrec == 3: cfg.recordCells = [(pop,50) for pop in ['IT5A', 'PT5B']]+[('PT5B',x) for x in [393,579,19,104]] #,214,1138,799]] # record selected cells # record selected cells
elif cfg.cellsrec == 4: cfg.recordCells = [(pop,50) for pop in ['IT2', 'IT4', 'IT5A', 'PT5B']]+[('PT5B',x) for x in [393,447,579,19,104,214,1138,979,799]] # record selected cells
 
cfg.recordTraces = {'V_soma': {'sec':'soma', 'loc':0.5, 'var':'v'}}#,
					# 'V_apic_23': {'sec':'apic_23', 'loc':0.5, 'var':'v', 'conds':{'pop': 'PT5B'}},
					# 'V_apic_26': {'sec':'apic_26', 'loc':0.5, 'var':'v', 'conds':{'pop': 'PT5B'}},
					# 'V_dend_5': {'sec':'dend_5', 'loc':0.5, 'var':'v', 'conds':{'pop': 'PT5B'}}}
					#'I_AMPA_Adend2': {'sec':'Adend2', 'loc':0.5, 'synMech': 'AMPA', 'var': 'i'}}

#cfg.recordLFP = [[150, y, 150] for y in range(200,1300,100)]

cfg.recordStim = False
cfg.recordTime = False  
cfg.recordStep = 0.1


#------------------------------------------------------------------------------
# Saving
#------------------------------------------------------------------------------
cfg.simLabel = 'sM1_02-08-2025_01'

cfg.saveFolder = 'data'
cfg.savePickle = False
cfg.saveJson = True
cfg.saveDataInclude = ['simData', 'simConfig', 'netParams', 'net']
cfg.backupCfgFile = None #['cfg.py', 'backupcfg/'] 
cfg.gatherOnlySimData = False
cfg.saveCellSecs = False
cfg.saveCellConns = False
cfg.compactConnFormat = 0

#------------------------------------------------------------------------------
# Analysis and plotting 
#------------------------------------------------------------------------------
with open('cells/popColors.pkl', 'rb') as fileObj: popColors = pickle.load(fileObj)['popColors']
#cfg.analysis['plotRaster'] = {'include': allpops, 'orderBy': ['pop', 'y'], 'timeRange': [0,60000], 'saveFig': True, 'showFig': False, 'labels': 'overlay', 'popRates': True, 'orderInverse': True, 
#							 'popColors': popColors, 'figSize': (12,10), 'lw': 0.3, 'markerSize':3, 'marker': '.', 'dpi': 300} 


#cfg.analysis['plotSpikeHist'] = {'include': ['IT2','IT4','IT5A','IT5B','PT5B','IT6','CT6'], 'timeRange': [0,60000], 'yaxis':'rate', 'binSize':5, 'graphType':'bar',
# 								'saveFig': True, 'showFig': False, 'popColors': popColors, 'figSize': (10,4), 'dpi': 300} 

#cfg.analysis['plotLFP'] = {'plots': ['timeSeries', 'PSD', 'spectrogram'], 'figSize': (6,10), 'timeRange': [0,60000], 'NFFT': 256*20, 'noverlap': 128*20, 'nperseg': 132*20, 
#							'saveFig': True, 'showFig':False} 


#cfg.analysis['plotTraces'] = {'include': [('IT5A',50), ('PT5B',50), ('PT5B',393), ('PT5B',579), ('PT5B',19), ('PT5B',104)], 'timeRange': [0,2000], 'oneFigPer': 'cell', 'figSize': (10,4), 'saveFig': True, 'showFig': False} 

#cfg.analysis['plotShape'] = {'includePre': ['all'], 'includePost': [('PT5B',100)], 'cvar':'numSyns','saveFig': True, 'showFig': False, 'includeAxon': False}
#cfg.analysis['plotConn'] = {'include': ['allCells']}
# cfg.analysis['calculateDisynaptic'] = True

# cfg.analysis['plotConn'] = {'includePre': allpops, 'includePost': allpops, 'feature': 'strength', 'figSize': (10,10), 'groupBy': 'pop', \
# 						'graphType': 'bar', 'synOrConn': 'conn', 'synMech': None, 'saveData': None, 'saveFig': 1, 'showFig': 0}

#------------------------------------------------------------------------------
# Cells
#------------------------------------------------------------------------------
cfg.cellmod =  {'IT2': 'HH_reduced',
				'IT4': 'HH_reduced',
				'IT5A': 'HH_full',
				'IT5B': 'HH_reduced',
				'PT5B': 'HH_full',
				'IT6': 'HH_reduced',
				'CT6': 'HH_reduced'}

cfg.ihModel = 'migliore'  # ih model
cfg.ihGbar = 1.0  # multiplicative factor for ih gbar in PT cells
cfg.ihGbarZD = None # multiplicative factor for ih gbar in PT cells
cfg.ihGbarBasal = 1.0 # 0.1 # multiplicative factor for ih gbar in PT cells
cfg.ihlkc = 0.2 # ih leak param (used in Migliore)
cfg.ihlkcBasal = 1.0
cfg.ihlkcBelowSoma = 0.01
cfg.ihlke = -86  # ih leak param (used in Migliore)
cfg.ihSlope = 14*2

cfg.removeNa = False  # simulate TTX; set gnabar=0s
cfg.somaNa = 5
cfg.dendNa = 0.3
cfg.axonNa = 7
cfg.axonRa = 0.005

cfg.gpas = 0.5  # multiplicative factor for pas g in PT cells
cfg.epas = 0.9  # multiplicative factor for pas e in PT cells

#------------------------------------------------------------------------------
# Synapses
#------------------------------------------------------------------------------
cfg.synWeightFractionEE = [0.5, 0.5] # E->E AMPA to NMDA ratio
cfg.synWeightFractionEI = [0.5, 0.5] # E->I AMPA to NMDA ratio
cfg.synWeightFractionSOME = [0.9, 0.1] # SOM -> E GABAASlow to GABAB ratio

cfg.synsperconn = {'HH_full': 5, 'HH_reduced': 1, 'HH_simple': 1}
cfg.AMPATau2Factor = 1.0

#------------------------------------------------------------------------------
# Network 
#------------------------------------------------------------------------------
cfg.singleCellPops = 0  # Create pops with 1 single cell (to debug)
cfg.weightNorm = 1  # use weight normalization
cfg.weightNormThreshold = 4.0  # weight normalization factor threshold

cfg.addConn = 1
cfg.scale = 1.0
cfg.sizeY = 1350.0
cfg.sizeX = 300.0
cfg.sizeZ = 300.0
cfg.correctBorderThreshold = 150.0

cfg.L5BrecurrentFactor = 1.0
cfg.ITinterFactor = 1.0
cfg.strengthFactor = 1.0

cfg.EEGain = 1.0
cfg.EIGain = 1.0
cfg.IEGain = 1.0
cfg.IIGain = 1.0

cfg.IEdisynapticBias = None  # increase prob of I->Ey conns if Ex->I and Ex->Ey exist 

#------------------------------------------------------------------------------
## E->I gains
cfg.EPVGain = 1.0
cfg.ESOMGain = 1.0

#------------------------------------------------------------------------------
## I->E gains
cfg.PVEGain = 1.0
cfg.SOMEGain = 1.0

#------------------------------------------------------------------------------
## I->I gains
cfg.PVSOMGain = None #0.25
cfg.SOMPVGain = None #0.25
cfg.PVPVGain = None # 0.75
cfg.SOMSOMGain = None #0.75

#------------------------------------------------------------------------------
## I->E/I layer weights (L2/3+4, L5, L6)
cfg.IEweights = [1.0, 1.0, 1.0]
cfg.IIweights = [1.0, 1.0, 1.0]

cfg.IPTGain = 1.0
cfg.IFullGain = 1.0

#------------------------------------------------------------------------------
# Subcellular distribution
#------------------------------------------------------------------------------
cfg.addSubConn = 1

#------------------------------------------------------------------------------
# Long range inputs
#------------------------------------------------------------------------------
cfg.addLongConn = 0
cfg.numCellsLong = 1000 # num of cells per population
cfg.noiseLong = 0.0  # firing rate random noise
cfg.delayLong = 5.0  # (ms)
cfg.weightLong = 0.0  # corresponds to unitary connection somatic EPSP (mV)
cfg.startLong = 0  # start at 0 ms
#cfg.ratesLong = {'TPO': [0,2], 'TVL': [0,2], 'S1': [0,2], 'S2': [0,2], 'cM1': [0,2], 'M2': [0,2], 'OC': [0,2]}


## input pulses
cfg.addPulses = 0
cfg.pulse = {'pop': 'None', 'start': 600000, 'end': 61000, 'rate': 0, 'noise': 0.0}
#cfg.pulse2 = {'pop': 'None', 'start': 60000, 'end': 61000, 'rate': 0, 'noise': 0.0, 'duration': None}


#------------------------------------------------------------------------------
# Current inputs 
#------------------------------------------------------------------------------
cfg.addIClamp = True

#cfg.IClamp1 = {'pop': 'IT5B', 'sec': 'soma', 'loc': 0.5, 'start': 0, 'dur': 1000, 'amp': 0.50}

cfg.IClamp1 = {'pop': '', 'sec': 'soma', 'loc': 0.5, 'start': 0, 'dur': 100, 'amp': 0.57}


#------------------------------------------------------------------------------
# NetStim inputs 
#------------------------------------------------------------------------------
cfg.addNetStim = 0

 			   ## pop, sec, loc, synMech, start, interval, noise, number, weight, delay 
# cfg.NetStim1 = {'pop': 'IT2', 'sec': 'soma', 'loc': 0.5, 'synMech': ['AMPA','NMDA'], 'synMechWeightFactor': cfg.synWeightFractionEE,
# 				'start': 500, 'interval': 50.0, 'noise': 0.2, 'number': 1000.0/50.0, 'weight': 10.0, 'delay': 1}
#cfg.NetStim1 = {'pop': 'IT2', 'ynorm':[0,1], 'sec': 'soma', 'loc': 0.5, 'synMech': ['AMPA'], 'synMechWeightFactor': [1.0],
#				'start': 500, 'interval': 1000.0/60.0, 'noise': 0.0, 'number': 60.0, 'weight': 30.0, 'delay': 0}