def makeAxonProto():
axon = moose.Neuron('/library/axon')
prev = rd.buildCompt(axon,
'soma',
RM=RM,
RA=RA,
CM=CM,
dia=10e-6,
x=0,
dx=comptLen)
theta = 0
x = comptLen
y = 0.0
for i in range(numAxonSegments):
dx = comptLen * np.cos(theta)
dy = comptLen * np.sin(theta)
r = np.sqrt(x * x + y * y)
theta += comptLen / r
compt = rd.buildCompt(axon,
'axon' + str(i),
RM=RM,
RA=RA,
CM=CM,
x=x,
y=y,
dx=dx,
dy=dy,
dia=comptDia)
moose.connect(prev, 'axial', compt, 'raxial')
prev = compt
x += dx
y += dy
return axon
def makeCellProto(name):
elec = moose.Neuron('/library/' + name)
ecompt = []
soma = rd.buildCompt(elec, 'soma', somaDia, somaDia, -somaDia, RM, RA, CM)
dend = rd.buildCompt(elec, 'dend', dendLen, dendDia, 0, RM, RA, CM)
moose.connect(soma, 'axial', dend, 'raxial')
elec.buildSegmentTree()
def makeCellProto( name ):
elec = moose.Neuron( '/library/' + name )
ecompt = []
soma = rd.buildCompt( elec, 'soma', somaDia, somaDia, -somaDia, RM, RA, CM )
dend = rd.buildCompt( elec, 'dend', dendLen, dendDia, 0, RM, RA, CM )
moose.connect( soma, 'axial', dend, 'raxial' )
elec.buildSegmentTree()
def makeDendProto():
dend=moose.Neuron('/library/dend')
#prev=rd.buildCompt(dend,'soma',RM=RM,RA=RA,CM=CM,dia=0.3e-06,x=0,dx=comptLenBuff)
prev=rd.buildCompt(dend,'soma',RM=RM,RA=RA,CM=CM,dia=0.3e-06,x=0,dx=comptLen)
#x=comptLenBuff
x=comptLen
y=0.0
comptDia=0.3e-06
for i in range(numDendSegments-1):
dx=comptLen
dy=0
#comptDia +=1.7e-08
compt=rd.buildCompt(dend,'dend'+str(i),RM=RM,RA=RA,CM=CM,x=x,y=y,dx=dx,dy=dy,dia=comptDia)
moose.connect(prev,'axial',compt,'raxial')
prev=compt
x+=dx
y+=dy
print i
for i in range(numDendSegments,numDendSegments+lenbfNotch):
print i
dx=comptLen
dy=0
comptDia -=0.5e-07
print comptDia
compt=rd.buildCompt(dend,'dend'+str(i),RM=RM,RA=RA,CM=CM,x=x,dx=dx,dy=dy,dia=comptDia)
moose.connect(prev,'axial',compt,'raxial')
prev=compt
x+=dx
y+=dy
for i in range(numDendSegments+lenbfNotch,numDendSegments+lenbfNotch+lenafNotch):
dx=comptLen
dy=0
comptDia +=0.5e-07
print comptDia
compt=rd.buildCompt(dend,'dend'+str(i),RM=RM,RA=RA,CM=CM,x=x,dx=dx,dy=dy,dia=comptDia)
moose.connect(prev,'axial',compt,'raxial')
prev=compt
x+=dx
y+=dy
for i in range (numDendSegments+lenbfNotch+lenafNotch,numDendSegments+lenbfNotch+lenafNotch+numDendSegmentsSlope):
dx=comptLen
dy=0
#comptDia -=0.1e-07
print comptDia
compt=rd.buildCompt(dend,'dend'+str(i),RM=RM,RA=RA,CM=CM,x=x,y=y,dx=dx,dy=dy,dia=comptDia)
moose.connect(prev,'axial',compt,'raxial')
prev=compt
x+=dx
y+=dy
#compt=rd.buildCompt(dend,'dendL',RM=RM,RA=RA,CM=CM,x=x,y=y,dx=comptLenBuff,dy=dy,dia=comptDia)
#moose.connect(prev,'axial',compt,'raxial')
return dend
def makeYmodel():
segLen = dendLength / numDendSeg
rdes = rd.rdesigneur(
stealCellFromLibrary=True,
verbose=False,
# cellProto syntax: ['ballAndStick', 'name', somaDia, somaLength, dendDia, dendLength, numDendSegments ]
# The numerical arguments are all optional
cellProto=[[
'ballAndStick', 'cellBase', dendDia, segLen, dendDia, dendLength,
numDendSeg
]],
passiveDistrib=[[
'#', 'RM',
str(dendRM), 'CM',
str(dendCM), 'RA',
str(dendRA)
]],
stimList=[['soma', '1', '.', 'inject', stimStr]],
)
# Build the arms of the Y for a branching cell.
pa = moose.element('/library/cellBase')
x = length
y = 0.0
dx = length / (numDendSeg * np.sqrt(2.0))
dy = dx
prevc1 = moose.element('/library/cellBase/dend{}'.format(numDendSeg - 1))
prevc2 = prevc1
for i in range(numDendSeg):
c1 = rd.buildCompt(pa,
'branch1_{}'.format(i),
RM=RM,
CM=CM,
RA=RA,
dia=dia,
x=x,
y=y,
dx=dx,
dy=dy)
c2 = rd.buildCompt(pa,
'branch2_{}'.format(i),
RM=RM,
CM=CM,
RA=RA,
dia=dia,
x=x,
y=-y,
dx=dx,
dy=-dy)
moose.connect(prevc1, 'axial', c1, 'raxial')
moose.connect(prevc2, 'axial', c2, 'raxial')
prevc1 = c1
prevc2 = c2
x += dx
y += dy
rdes.buildModel()
def makeDendProto():
dend = moose.Neuron('/library/dend')
prev = rd.buildCompt(dend,
'soma',
RM=RM,
RA=RA,
CM=CM,
dia=10e-06,
x=0,
dx=comptLenBuff)
x = comptLenBuff
y = 0.0
comptDia = 10e-06
for i in range(numDendSegments):
dx = comptLen
dy = 0
#comptDia +=1.7e-08
compt = rd.buildCompt(dend,
'dend' + str(i),
RM=RM,
RA=RA,
CM=CM,
x=x,
y=y,
dx=dx,
dy=dy,
dia=comptDia)
moose.connect(prev, 'axial', compt, 'raxial')
prev = compt
x += dx
y += dy
compt = rd.buildCompt(dend,
'dendL',
RM=RM,
RA=RA,
CM=CM,
x=x,
y=y,
dx=comptLenBuff,
dy=dy,
dia=comptDia)
moose.connect(prev, 'axial', compt, 'raxial')
return dend
def makeAxonProto():
axon = moose.Neuron( '/library/axon' )
prev = rd.buildCompt( axon, 'soma', RM = RM, RA = RA, CM = CM, dia = 10e-6, x=0, dx=comptLen)
theta = 0
x = comptLen
y = 0.0
for i in range( numAxonSegments ):
dx = comptLen * np.cos( theta )
dy = comptLen * np.sin( theta )
r = np.sqrt( x * x + y * y )
theta += comptLen / r
compt = rd.buildCompt( axon, 'axon' + str(i), RM = RM, RA = RA, CM = CM, x = x, y = y, dx = dx, dy = dy, dia = comptDia )
moose.connect( prev, 'axial', compt, 'raxial' )
prev = compt
x += dx
y += dy
return axon
def makeCellProto(name):
elec = moose.Neuron('/library/' + name)
ecompt = []
ec = rd.buildCompt(elec,
'dend',
dx=dendLen,
dia=2.0e-6,
x=0,
RM=RM,
RA=RA,
CM=CM)
elec.buildSegmentTree()
def makeSpineProto2(name):
spine = moose.Neutral('/library/' + name)
shaft = rd.buildCompt(spine,
'shaft',
dz=1e-6,
dx=0,
dia=0.2e-6,
z=0,
RM=RM,
RA=RA,
CM=CM)
head = rd.buildCompt(spine,
'head',
dz=0.5e-6,
dx=0,
dia=0.5e-6,
z=1e-6,
RM=RM,
RA=RA,
CM=CM)
moose.connect(shaft, 'axial', head, 'raxial')
def makeCellProto(name):
elec = moose.Neuron('/library/' + name)
ecompt = []
###soma = rd.buildCompt( elec, 'soma', dx=somaDia, dia=somaDia, x=-somaDia, RM=RM, RA=RA, CM=CM )
dend = rd.buildCompt(elec,
'dend',
dx=dendLen,
dia=dendDia,
x=0,
RM=RM,
RA=RA,
CM=CM)
###moose.connect( soma, 'axial', dend, 'raxial' )
elec.buildSegmentTree()
def makeCellProto( name ):
print(('IN: makeCellProto( ', name, ')'))
elec = moose.Neuron( '/library/' + name )
ecompt = []
for i in range( numDendSegments ):
ec = rd.buildCompt( elec, 'dend' + str(i), segLen, 2.0e-6, i * segLen, RM, RA, CM )
ecompt.append( ec )
if i > 0:
moose.connect( ecompt[i-1], 'axial', ec, 'raxial' )
else:
ec.name = "soma"
for i in ecompt:
i.z0 = i.x0
i.x0 = 0
i.z = i.x
i.x = 0
def makeCellProto(name):
print(('IN: makeCellProto( ', name, ')'))
elec = moose.Neuron('/library/' + name)
ecompt = []
for i in range(numDendSegments):
ec = rd.buildCompt(elec, 'dend' + str(i), segLen, 2.0e-6, i * segLen,
RM, RA, CM)
ecompt.append(ec)
if i > 0:
moose.connect(ecompt[i - 1], 'axial', ec, 'raxial')
else:
ec.name = "soma"
for i in ecompt:
i.z0 = i.x0
i.x0 = 0
i.z = i.x
i.x = 0
def makeSpineProto2( name ):
spine = moose.Neutral( '/library/' + name )
shaft = rd.buildCompt( spine, 'shaft', 0.5e-6, 0.4e-6, 0, RM, RA, CM )
head = rd.buildCompt( spine, 'head', 0.5e-6, 0.5e-6, 0.5e-6, RM, RA, CM )
moose.connect( shaft, 'axial', head, 'raxial' )
def makeSpineProto2( name ):
spine = moose.Neutral( '/library/' + name )
shaft = rd.buildCompt( spine, 'shaft', dz=1e-6, dx = 0, dia=0.2e-6, z=0, RM=RM, RA=RA, CM=CM )
head = rd.buildCompt( spine, 'head', dz=0.5e-6, dx = 0, dia=0.5e-6, z=1e-6, RM=RM, RA=RA, CM=CM )
moose.connect( shaft, 'axial', head, 'raxial' )
def makeCellProto( name ):
elec = moose.Neuron( '/library/' + name )
ecompt = []
ec = rd.buildCompt( elec, 'dend', dendLen, 2.0e-6, 0, RM, RA, CM )
elec.buildSegmentTree()
def makeYmodel():
length = rec[0].geom
dia = rec[3].geom
segLen = length / numDendSeg
cp = [['make_glu()', 'glu'], ['make_GABA()', 'GABA']]
cp.extend(spikingProto)
cd = [['glu', 'dend9', 'Gbar', str(rec[0].Gbar)],
['glu', 'branch1_9', 'Gbar',
str(rec[1].Gbar)], ['glu', 'branch2_9', 'Gbar',
str(rec[2].Gbar)],
['GABA', 'dend9', 'Gbar', str(rec[3].Gbar)],
['GABA', 'branch1_9', 'Gbar',
str(rec[4].Gbar)], ['GABA', 'branch2_9', 'Gbar',
str(rec[5].Gbar)]]
cd.extend(spikingDistrib)
rdes = rd.rdesigneur(
elecPlotDt=elecPlotDt,
stealCellFromLibrary=True,
verbose=False,
#chanProto = [['make_glu()', 'glu'],['make_GABA()', 'GABA']],
chanProto=cp,
# cellProto syntax: ['ballAndStick', 'name', somaDia, somaLength, dendDia, dendLength, numDendSegments ]
# The numerical arguments are all optional
cellProto=[[
'ballAndStick', 'cellBase', dia, segLen, dia, length, numDendSeg
]],
passiveDistrib=[['#', 'RM',
str(RM), 'CM',
str(CM), 'RA',
str(RA)]],
chanDistrib=cd,
#chanDistrib = [
#['glu', 'dend9', 'Gbar', str(rec[0].Gbar)],
#['glu', 'branch1_9', 'Gbar', str(rec[1].Gbar)],
#['glu', 'branch2_9', 'Gbar', str(rec[2].Gbar)],
#['GABA', 'dend9', 'Gbar', str(rec[3].Gbar)],
#['GABA', 'branch1_9', 'Gbar', str(rec[4].Gbar)],
#['GABA', 'branch2_9', 'Gbar', str(rec[5].Gbar)],
#],
stimList=[
[
'dend9', '1', 'glu', 'periodicsyn',
'{}*(t>{:.3f} && t<{:.3f})'.format(
rec[0].inputFreq, rec[0].onset,
rec[0].onset + rec[0].inputDuration)
],
[
'branch1_9', '1', 'glu', 'periodicsyn',
'{}*(t>{:.3f} && t<{:.3f})'.format(
rec[1].inputFreq, rec[1].onset,
rec[1].onset + rec[1].inputDuration)
],
[
'branch2_9', '1', 'glu', 'periodicsyn',
'{}*(t>{:.3f} && t<{:.3f})'.format(
rec[2].inputFreq, rec[2].onset,
rec[2].onset + rec[2].inputDuration)
],
[
'dend9', '1', 'GABA', 'periodicsyn',
'{}*(t>{:.3f} && t<{:.3f})'.format(
rec[3].inputFreq, rec[3].onset,
rec[3].onset + rec[3].inputDuration)
],
[
'branch1_9', '1', 'GABA', 'periodicsyn',
'{}*(t>{:.3f} && t<{:.3f})'.format(
rec[4].inputFreq, rec[4].onset,
rec[4].onset + rec[4].inputDuration)
],
[
'branch2_9', '1', 'GABA', 'periodicsyn',
'{}*(t>{:.3f} && t<{:.3f})'.format(
rec[5].inputFreq, rec[5].onset,
rec[5].onset + rec[5].inputDuration)
],
#['dend9,branch1_9,branch2_9', '1','glu', 'periodicsyn', '100*(t>0.01 && t<0.02)'],
],
plotList=[
['soma,dend9,branch1_9,branch2_9', '1', '.', 'Vm'],
],
)
# Modify some library values based on the slider controls
glu = moose.element('/library/glu')
gaba = moose.element('/library/GABA')
glu.tau1 = rec[0].tau1
glu.tau2 = rec[1].tau2
glu.Ek = rec[2].Ek
gaba.tau1 = rec[3].tau1
gaba.tau2 = rec[4].tau2
gaba.Ek = rec[5].Ek
# Build the arms of the Y for a branching cell.
pa = moose.element('/library/cellBase')
x1 = length
x2 = length
y1 = 0.0
y2 = 0.0
dx1 = rec[1].geom / (numDendSeg * np.sqrt(2.0))
dx2 = rec[2].geom / (numDendSeg * np.sqrt(2.0))
dia1 = rec[4].geom
dia2 = rec[5].geom
dy1 = dx1
dy2 = -dx2
prevc1 = moose.element('/library/cellBase/dend{}'.format(numDendSeg - 1))
prevc2 = prevc1
for i in range(numDendSeg):
c1 = rd.buildCompt(pa,
'branch1_{}'.format(i),
RM=RM,
CM=CM,
RA=RA,
dia=dia1,
x=x1,
y=y1,
dx=dx1,
dy=dy1)
c2 = rd.buildCompt(pa,
'branch2_{}'.format(i),
RM=RM,
CM=CM,
RA=RA,
dia=dia2,
x=x2,
y=y2,
dx=dx2,
dy=dy2)
moose.connect(prevc1, 'axial', c1, 'raxial')
moose.connect(prevc2, 'axial', c2, 'raxial')
prevc1 = c1
prevc2 = c2
x1 += dx1
y1 += dy1
x2 += dx2
y2 += dy2
rdes.elecid.buildSegmentTree() # rebuild it as we've added the branches
rdes.buildModel()
# Permit fast spiking input.
#for i in moose.wildcardFind( '/model/##[ISA=RandSpike]' ):
for i in moose.wildcardFind('/model/elec/#/#/#/#/synInput_rs'):
#print i.path, i.refractT
i.refractT = 0.002
'''
def makeYmodel():
length = rec[0].geom
dia = rec[3].geom
segLen = length / numDendSeg
cp = [['make_glu()', 'glu'],['make_GABA()', 'GABA']]
cp.extend( spikingProto )
cd = [
['glu', 'dend9', 'Gbar', str(rec[0].Gbar)],
['glu', 'branch1_9', 'Gbar', str(rec[1].Gbar)],
['glu', 'branch2_9', 'Gbar', str(rec[2].Gbar)],
['GABA', 'dend9', 'Gbar', str(rec[3].Gbar)],
['GABA', 'branch1_9', 'Gbar', str(rec[4].Gbar)],
['GABA', 'branch2_9', 'Gbar', str(rec[5].Gbar)]
]
cd.extend( spikingDistrib )
rdes = rd.rdesigneur(
elecPlotDt = elecPlotDt,
stealCellFromLibrary = True,
verbose = False,
#chanProto = [['make_glu()', 'glu'],['make_GABA()', 'GABA']],
chanProto = cp,
# cellProto syntax: ['ballAndStick', 'name', somaDia, somaLength, dendDia, dendLength, numDendSegments ]
# The numerical arguments are all optional
cellProto =
[['ballAndStick', 'cellBase', dia, segLen, dia, length, numDendSeg]],
passiveDistrib = [[ '#', 'RM', str(RM), 'CM', str(CM), 'RA', str(RA) ]],
chanDistrib = cd,
#chanDistrib = [
#['glu', 'dend9', 'Gbar', str(rec[0].Gbar)],
#['glu', 'branch1_9', 'Gbar', str(rec[1].Gbar)],
#['glu', 'branch2_9', 'Gbar', str(rec[2].Gbar)],
#['GABA', 'dend9', 'Gbar', str(rec[3].Gbar)],
#['GABA', 'branch1_9', 'Gbar', str(rec[4].Gbar)],
#['GABA', 'branch2_9', 'Gbar', str(rec[5].Gbar)],
#],
stimList = [
['dend9', '1','glu', 'periodicsyn', '{}*(t>{:.3f} && t<{:.3f})'.format( rec[0].inputFreq, rec[0].onset, rec[0].onset + rec[0].inputDuration) ],
['branch1_9', '1','glu', 'periodicsyn', '{}*(t>{:.3f} && t<{:.3f})'.format( rec[1].inputFreq, rec[1].onset, rec[1].onset + rec[1].inputDuration) ],
['branch2_9', '1','glu', 'periodicsyn', '{}*(t>{:.3f} && t<{:.3f})'.format( rec[2].inputFreq, rec[2].onset, rec[2].onset + rec[2].inputDuration) ],
['dend9', '1','GABA', 'periodicsyn', '{}*(t>{:.3f} && t<{:.3f})'.format( rec[3].inputFreq, rec[3].onset, rec[3].onset + rec[3].inputDuration) ],
['branch1_9', '1','GABA', 'periodicsyn', '{}*(t>{:.3f} && t<{:.3f})'.format( rec[4].inputFreq, rec[4].onset, rec[4].onset + rec[4].inputDuration) ],
['branch2_9', '1','GABA', 'periodicsyn', '{}*(t>{:.3f} && t<{:.3f})'.format( rec[5].inputFreq, rec[5].onset, rec[5].onset + rec[5].inputDuration) ],
#['dend9,branch1_9,branch2_9', '1','glu', 'periodicsyn', '100*(t>0.01 && t<0.02)'],
],
plotList = [
['soma,dend9,branch1_9,branch2_9', '1','.', 'Vm'],
],
)
# Modify some library values based on the slider controls
glu = moose.element( '/library/glu' )
gaba = moose.element( '/library/GABA' )
glu.tau1 = rec[0].tau1
glu.tau2 = rec[1].tau2
glu.Ek = rec[2].Ek
gaba.tau1 = rec[3].tau1
gaba.tau2 = rec[4].tau2
gaba.Ek = rec[5].Ek
# Build the arms of the Y for a branching cell.
pa = moose.element( '/library/cellBase' )
x1 = length
x2 = length
y1 = 0.0
y2 = 0.0
dx1 = rec[1].geom / ( numDendSeg * np.sqrt(2.0) )
dx2 = rec[2].geom / ( numDendSeg * np.sqrt(2.0) )
dia1 = rec[4].geom
dia2 = rec[5].geom
dy1 = dx1
dy2 = -dx2
prevc1 = moose.element( '/library/cellBase/dend{}'.format( numDendSeg-1 ) )
prevc2 = prevc1
for i in range( numDendSeg ):
c1 = rd.buildCompt( pa, 'branch1_{}'.format(i), RM = RM, CM = CM, RA = RA, dia = dia1, x=x1, y=y1, dx = dx1, dy = dy1 )
c2 = rd.buildCompt( pa, 'branch2_{}'.format(i), RM = RM, CM = CM, RA = RA, dia = dia2, x=x2, y=y2, dx = dx2, dy = dy2 )
moose.connect( prevc1, 'axial', c1, 'raxial' )
moose.connect( prevc2, 'axial', c2, 'raxial' )
prevc1 = c1
prevc2 = c2
x1 += dx1
y1 += dy1
x2 += dx2
y2 += dy2
rdes.elecid.buildSegmentTree() # rebuild it as we've added the branches
rdes.buildModel()
# Permit fast spiking input.
#for i in moose.wildcardFind( '/model/##[ISA=RandSpike]' ):
for i in moose.wildcardFind( '/model/elec/#/#/#/#/synInput_rs' ):
#print i.path, i.refractT
i.refractT = 0.002
'''
