Computer models of corticospinal neurons replicate in vitro dynamics (Neymotin et al. 2017)

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Accession:195615
"Corticospinal neurons (SPI), thick-tufted pyramidal neurons in motor cortex layer 5B that project caudally via the medullary pyramids, display distinct class-specific electrophysiological properties in vitro: strong sag with hyperpolarization, lack of adaptation, and a nearly linear frequency-current (FI) relationship. We used our electrophysiological data to produce a pair of large archives of SPI neuron computer models in two model classes: 1. Detailed models with full reconstruction; 2. Simplified models with 6 compartments. We used a PRAXIS and an evolutionary multiobjective optimization (EMO) in sequence to determine ion channel conductances. ..."
Reference:
1 . Neymotin SA, Suter BA, Dura-Bernal S, Shepherd GM, Migliore M, Lytton WW (2017) Optimizing computer models of corticospinal neurons to replicate in vitro dynamics. J Neurophysiol 117:148-162 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex M1 L5B pyramidal pyramidal tract GLU cell; Neocortex primary motor area pyramidal layer 5 corticospinal cell;
Channel(s): I A; I h; I_KD; I K,Ca; I L high threshold; I Na,t; I N; Ca pump; Kir;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; Python;
Model Concept(s): Parameter Fitting; Activity Patterns; Active Dendrites; Detailed Neuronal Models; Simplified Models;
Implementer(s): Suter, Benjamin ; Neymotin, Sam [Samuel.Neymotin at nki.rfmh.org]; Dura-Bernal, Salvador [salvadordura at gmail.com]; Forzano, Ernie ;
Search NeuronDB for information about:  Neocortex M1 L5B pyramidal pyramidal tract GLU cell; I Na,t; I L high threshold; I N; I A; I h; I K,Ca; I_KD; Ca pump; Kir;
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spidemo
data
readme.html
cadad.mod
cal2.mod
can_mig.mod
h_kole.mod
kap_BS.mod
kBK.mod
kdmc_BS.mod
kdr_BS.mod
misc.mod *
nax_BS.mod
savedist.mod
vecst.mod *
archfig.py
axonMorph.py
BS0284.ASC
BS0409.ASC
conf.py
Fig6.py
figure_1.png
misc.h
morph.py
mosinit.py
PTcell.BS0284.cfg *
PTcell.BS0409.cfg
PTcell.cfg *
sim.py
SPI6.cfg
SPI6.py
utils.py
                            
"""
utils.py 

Useful functions related to the parameters file

Contributors: salvador dura@gmail.com 
"""
import os, sys
from neuron import h


def getSecName (sec, dirCellSecNames = None):
    if dirCellSecNames is None: dirCellSecNames = {}

    if '>.' in sec.name():
        fullSecName = sec.name().split('>.')[1] 
    elif '.' in sec.name():
        fullSecName = sec.name().split('.')[1]  
    else:
        fullSecName = sec.name()
    if '[' in fullSecName:  # if section is array element
        secNameTemp = fullSecName.split('[')[0]
        secIndex = int(fullSecName.split('[')[1].split(']')[0])
        secName = secNameTemp+'_'+str(secIndex) #(secNameTemp,secIndex)
    else:
        secName = fullSecName
        secIndex = -1
    if secName in dirCellSecNames:  # get sec names from python
        secName = dirCellSecNames[secName]
    return secName

def importCellParams (fileName, labels, values, key = None):
    params = {}
    if fileName.endswith('.py'):
        try:
            filePath,fileNameOnly = os.path.split(fileName)  # split path from filename
            if filePath not in sys.path:  # add to path if not there (need to import module)
                sys.path.insert(0, filePath)
            moduleName = fileNameOnly.split('.py')[0]  # remove .py to obtain module name
            exec('import '+ moduleName + ' as tempModule') in locals() # import module dynamically
            modulePointer = tempModule
            paramLabels = getattr(modulePointer, labels) # tuple with labels
            paramValues = getattr(modulePointer, values)  # variable with paramValues
            if key:  # if paramValues = dict
                paramValues = paramValues[key]
            params = dict(zip(paramLabels, paramValues))
            sys.path.remove(filePath)
        except:
            print "Error loading cell parameter values from " + fileName
    else:
        print "Trying to import izhi params from a file without the .py extension"
    return params


def mechVarList ():
    msname = h.ref('')
    varList = {}
    for i, mechtype in enumerate(['mechs','pointps']):
        mt = h.MechanismType(i)  # either distributed mechs (0) or point process (1)
        varList[mechtype] = {}
        for j in xrange(int(mt.count())):
            mt.select(j)
            mt.selected(msname)
            ms = h.MechanismStandard(msname[0], 1) # PARAMETER (modifiable)
            varList[mechtype][msname[0]] = []
            propName = h.ref('')
            for var in xrange(int(ms.count())):
                k = ms.name(propName, var)
                varList[mechtype][msname[0]].append(propName[0])
    return varList

def _equal_dicts (d1, d2, ignore_keys):
    ignored = set(ignore_keys)
    for k1, v1 in d1.iteritems():
        if k1 not in ignored and (k1 not in d2 or d2[k1] != v1):
            return False
    for k2, v2 in d2.iteritems():
        if k2 not in ignored and k2 not in d1:
            return False
    return True


def importCell (fileName, cellName, cellArgs = None):
    h.initnrn()

    if cellArgs is None: cellArgs = [] # Define as empty list if not otherwise defined

    ''' Import cell from HOC template or python file into framework format (dict of sections, with geom, topol, mechs, syns)'''
    if fileName.endswith('.hoc'):
        h.load_file(fileName)
        if isinstance(cellArgs, dict):
            cell = getattr(h, cellName)(**cellArgs)  # create cell using template, passing dict with args
        else:
            cell = getattr(h, cellName)(*cellArgs) # create cell using template, passing list with args
    elif fileName.endswith('.py'):
        filePath,fileNameOnly = os.path.split(fileName)  # split path from filename
        if filePath not in sys.path:  # add to path if not there (need to import module)
            sys.path.insert(0, filePath)
        moduleName = fileNameOnly.split('.py')[0]  # remove .py to obtain module name
        exec('import ' + moduleName + ' as tempModule') in globals(), locals() # import module dynamically
        modulePointer = tempModule
        if isinstance(cellArgs, dict):
            cell = getattr(modulePointer, cellName)(**cellArgs) # create cell using template, passing dict with args
        else:
            cell = getattr(modulePointer, cellName)(*cellArgs)  # create cell using template, passing list with args
        sys.path.remove(filePath)
    else:
        print "File name should be either .hoc or .py file"
        return

    secDic, secListDic, synMechs = getCellParams(cell)
    return secDic, secListDic, synMechs


def importCellsFromNet (netParams, fileName, labelList, condsList, cellNamesList, importSynMechs):
    h.initnrn()

    ''' Import cell from HOC template or python file into framework format (dict of sections, with geom, topol, mechs, syns)'''
    if fileName.endswith('.hoc'):
        print 'Importing from .hoc network not yet supported'
        return
        # h.load_file(fileName)
        # for cellName in cellNames:
        #     cell = getattr(h, cellName) # create cell using template, passing dict with args
        #     secDic, secListDic, synMechs = getCellParams(cell)

    elif fileName.endswith('.py'):
        origDir = os.getcwd()
        filePath,fileNameOnly = os.path.split(fileName)  # split path from filename
        if filePath not in sys.path:  # add to path if not there (need to import module)
            sys.path.insert(0, filePath)
        moduleName = fileNameOnly.split('.py')[0]  # remove .py to obtain module name
        os.chdir(filePath)
        print '\nRunning network in %s to import cells into NetPyNE ...\n'%(fileName)
        print h.name_declared('hcurrent')
        from neuron import load_mechanisms
        load_mechanisms(filePath)
        exec('import ' + moduleName + ' as tempModule') in globals(), locals() # import module dynamically
        modulePointer = tempModule
        sys.path.remove(filePath)
    else:
        print "File name should be either .hoc or .py file"
        return

    for label, conds, cellName in zip(labelList, condsList, cellNamesList):
        print '\nImporting %s from %s ...'%(cellName, fileName)
        exec('cell = tempModule' + '.' + cellName)
        #cell = getattr(modulePointer, cellName) # get cell object
        secs, secLists, synMechs = getCellParams(cell)
        cellRule = {'conds': conds, 'secs': secs, 'secLists': secLists}
        netParams.addCellParams(label, cellRule)
        if importSynMechs:
            for synMech in synMechs: netParams.addSynMechParams(synMech.pop('label'), synMech)


def getCellParams(cell):
    dirCell = dir(cell)

    if 'all_sec' in dirCell:
        secs = cell.all_sec
    elif 'sec' in dirCell:
        secs = [cell.sec]
    elif 'allsec' in dir(h):
        secs = [sec for sec in h.allsec()]
    elif 'soma' in dirCell:
        secs = [cell.soma]
    else:
        secs = []
    

    # create dict with hname of each element in dir(cell)
    dirCellHnames = {}  
    for dirCellName in dirCell:
        try:
            dirCellHnames.update({getattr(cell, dirCellName).hname(): dirCellName})
        except:
            pass
    # create dict with dir(cell) name corresponding to each hname 
    dirCellSecNames = {} 
    for sec in secs:
        dirCellSecNames.update({hname: name for hname,name in dirCellHnames.iteritems() if hname == sec.hname()})

    secDic = {}
    synMechs = []
    for sec in secs: 
        # create new section dict with name of section
        secName = getSecName(sec, dirCellSecNames)

        if len(secs) == 1:
            secName = 'soma' # if just one section rename to 'soma'
        secDic[secName] = {'geom': {}, 'topol': {}, 'mechs': {}}  # create dictionary to store sec info

        # store geometry properties
        standardGeomParams = ['L', 'nseg', 'diam', 'Ra', 'cm']
        secDir = dir(sec)
        for geomParam in standardGeomParams:
            #if geomParam in secDir:
            try:
                secDic[secName]['geom'][geomParam] = sec.__getattribute__(geomParam)
            except:
                pass

        # store 3d geometry
        numPoints = int(h.n3d())
        if numPoints: 
            points = []
            for ipoint in range(numPoints):
                x = h.x3d(ipoint)
                y = h.y3d(ipoint)
                z = h.z3d(ipoint)
                diam = h.diam3d(ipoint)
                points.append((x, y, z, diam))
            secDic[secName]['geom']['pt3d'] = points

        # store mechanisms
        varList = mechVarList()  # list of properties for all density mechanisms and point processes
        ignoreMechs = ['dist']  # dist only used during cell creation 
        mechDic = {}
        sec.push()  # access current section so ismembrane() works
        for mech in dir(sec(0.5)): 
            if h.ismembrane(mech) and mech not in ignoreMechs:  # check if membrane mechanism
                mechDic[mech] = {}  # create dic for mechanism properties
                varNames = [varName.replace('_'+mech, '') for varName in varList['mechs'][mech]]
                varVals = []
                for varName in varNames:
                    try:
                        varVals = [seg.__getattribute__(mech).__getattribute__(varName) for seg in sec]
                        if len(set(varVals)) == 1:
                            varVals = varVals[0] 
                        mechDic[mech][varName] = varVals
                    except: 
                        pass
                        #print 'Could not read variable %s from mechanism %s'%(varName,mech)

        secDic[secName]['mechs'] = mechDic

        # add synapses and point neurons
        # for now read fixed params, but need to find way to read only synapse params
        
        pointps = {}
        for seg in sec:
            for ipoint,point in enumerate(seg.point_processes()):
                pointpMod = point.hname().split('[')[0]
                varNames = varList['pointps'][pointpMod]
                if any([s in pointpMod.lower() for s in ['syn', 'ampa', 'gaba', 'nmda', 'glu']]):
                #if 'synMech' in pptype.lower(): # if syn in name of point process then assume synapse
                    synMech = {}
                    synMech['label'] = pointpMod + '_' + str(len(synMechs))
                    synMech['mod'] = pointpMod
                    #synMech['loc'] = seg.x
                    for varName in varNames:
                        try:
                            synMech[varName] = point.__getattribute__(varName)
                        except:
                            print 'Could not read variable %s from synapse %s'%(varName,synMech['label'])

                    if not [_equal_dicts(synMech, synMech2, ignore_keys=['label']) for synMech2 in synMechs]:
                        synMechs.append(synMech)
                
                else: # assume its a non-synapse point process
                    pointpName = pointpMod + '_'+ str(len(pointps))
                    pointps[pointpName] = {}
                    pointps[pointpName]['mod'] = pointpMod
                    pointps[pointpName]['loc'] = seg.x
                    for varName in varNames:
                        try:
                            pointps[pointpName][varName] = point.__getattribute__(varName)
                            # special condition for Izhi model, to set vinit=vr
                            # if varName == 'vr': secDic[secName]['vinit'] = point.__getattribute__(varName) 
                        except:
                            print 'Could not read %s variable from point process %s'%(varName,pointpName)

        if pointps: secDic[secName]['pointps'] = pointps

        # store topology (keep at the end since h.SectionRef messes remaining loop)
        secRef = h.SectionRef(sec=sec)
        if secRef.has_parent():
            secDic[secName]['topol']['parentSec'] = getSecName(secRef.parent().sec, dirCellSecNames)
            secDic[secName]['topol']['parentX'] = h.parent_connection()
            secDic[secName]['topol']['childX'] = h.section_orientation()

        h.pop_section()  # to prevent section stack overflow

    # # store synMechs in input argument
    # if synMechs: 
    #     for synMech in synMechs: synMechParams.append(synMech)
        
    # store section lists
    secLists = h.List('SectionList')
    if int(secLists.count()): 
        secListDic = {}
        for i in xrange(int(secLists.count())):  # loop over section lists
            hname = secLists.o(i).hname()
            if hname in dirCellHnames:  # use python variable name
                secListName = dirCellHnames[hname]
            else:
                secListName = hname
            secListDic[secListName] = [getSecName(sec, dirCellSecNames) for sec in secLists.o(i)]
    else:
        secListDic = {}

    # celsius warning
    if hasattr(h, 'celsius'):
        if h.celsius != 6.3:  # if not default value
            print "Warning: h.celsius=%.4g in imported file -- you can set this value in simConfig['hParams']['celsius']"%(h.celsius)

    # clean 
    h.initnrn()
    del(cell) # delete cell
    import gc; gc.collect()

    return secDic, secListDic, synMechs

    # cellRule['secs'] = secDic
    # if secListDic:
    #     cellRule['secLists'] = secListDic


# dictionary to translate params, fitness functions into more readable form - sam n
dtrans = {}
dtrans['FI'] = 'FI'
dtrans['ISIVolt'] = 'ISI Voltage'
dtrans['InstRate'] = 'Inst Rate'
dtrans['SpikeShape'] = 'Spike Shape'
dtrans['SpikePeak'] = 'Spike Peak'
dtrans['SpikeW'] = 'Spike Width'
dtrans['SpikeSlope'] = 'Spike Slope'
dtrans['SpikeThresh'] = 'Spike Thresh'
dtrans['VoltDiff'] = 'Subthresh Volt'
dtrans['morph.nax_gbar'] = dtrans['SPI6.gbar_nax'] = r'$\bar g_{Na}$'
dtrans['morph.kBK_caVhminShift'] = dtrans['SPI6.kBK_caVhminShift'] = r'$Shift_{BK}$'
dtrans['morph.cadad_taur'] = dtrans['SPI6.cadad_taur'] = r'$\tau_{Ca}$'
dtrans['morph.kdr_gbar'] = dtrans['SPI6.gbar_kdr'] = r'$\bar g_{Kdr}$'
dtrans['morph.cal_gcalbar'] = dtrans['SPI6.cal_gcalbar'] = r'$\bar p_L$'
dtrans['morph.kBK_gpeak'] = dtrans['SPI6.kBK_gpeak'] = r'$\bar g_{BK}$'
dtrans['morph.kap_gbar'] = dtrans['SPI6.gbar_kap'] = r'$\bar g_{KA}$'
dtrans['morph.can_gcanbar'] = dtrans['SPI6.can_gcanbar'] = r'$\bar p_N$'
dtrans['morph.kdmc_gbar'] = dtrans['SPI6.gbar_kdmc'] = r'$\bar g_{KD}$'
dtrans['morph.cadad_depth'] = dtrans['SPI6.cadad_depth'] = r'$depth_{Ca}$'
dtrans['SPI6.kap_vhalfl'] = r'$v1/2l_{KA}$'
dtrans['SPI6.kap_vhalfn'] = r'$v1/2n_{KA}$'
dtrans['SPI6.kap_tq'] = 'h.tq_kap'
dtrans['SPI6.kdr_vhalfn'] = r'$v1/2n_{Kdr}$'


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