from neuron import h
import nrnutils_ss as nu
class Spine():
def __init__(self,
name,
p,
neck_mechanisms = [],
head_mechanisms = [],
parent = None,
connection_point = 0,
noiseRandObj = None,
balance_currents=False,
highindex=None):
self.name = name
self.parent_sec = parent[0]
self.parent_seg = parent[1]
self.parent_x = parent[1].x
# Spine morphology from Kater & Harris 1994
# neck: 0.2 < L < 2 um, 0.04 < diam < 0.5 um, 2.512e-4 < volume < 0.3925 um3, 0.00112 < surface < 3.14 um2
# total: 0.004 < volume < 0.6 um3, 0.1 < surface < 4 um2
# spine: 3.7488e-3 < volume < 0.2075 um3, 0.09888 < surface < 0.86 um2
# spine: diam = 1 um -> L = v/((diam/2)^2*3.14) = 0.2075/0.785 = 0.264 um -> surface = 0.82896 um2
# we use here:
# neck: L = 1 um, diam = 0.1 um
# head: L = 0.264 um, diam = 1 um, v = 0.2075 um3
# the head volume could be reduced
self.neck = nu.Section(
'neck',
L=2,
diam=0.5,
cm = p['CmDend'],
Ra = p['RaAll'],
mechanisms=neck_mechanisms,
parent = self.parent_sec,
connection_point = self.parent_x)
self.head = nu.Section(
'head',
L=0.264,
diam=1,
cm = p['CmDend'],
Ra = p['RaAll'],
mechanisms=head_mechanisms,
parent = self.neck,
point_processes=p['spine_point_processes'],
records=p['spine_records'])
# self.parent_sec.push()
# for m,attr in [['na3','gbar_na3'],
# ['kdr','gkdrbar_kdr'],
# ['kad','gkabar_kad']]:
# if h.ismembrane(m):
# setattr(self.head,attr, getattr(self.parent_sec,attr))
# print getattr(self.head,attr)
# h.pop_section()
# Access head section
self.head.push()
# print self.head.BDNF.alpha_gAMPA, self.head.BDNF.theta_gAMPA, self.head.BDNF.sigma_gAMPA
if hasattr(self.head, 'BDNF'):
self.head.BDNF.setRandObjRef(noiseRandObj)
self.highindex = noiseRandObj.MCellRan4(highindex)
if h.ismembrane('ca_ion'):
setattr(self.head,'internal_nc',h.NetCon(self.head(0.5)._ref_cai, self.head.BDNF, sec = self.head))
self.head.internal_nc.threshold = self.head.BDNF.theta_cai_BDNF
# print 'theta_cai_BDNF', self.head.internal_nc.threshold
self.head.internal_nc.delay = 0.1e-3
else:
raise Exception("BDNF mechanism requires also cad for Ca dynamics")
if hasattr(self.head, 'AMPA'):
if p['check']:
print("Setting pointer AMPA.g_factor->BDNF.gAMPA")
h.setpointer(self.head.AMPA._ref_g_factor, 'gAMPA', self.head.BDNF)
else:
raise Exception("BDNF mechanism require also AMPA")
if hasattr(self.head, 'RMECB'):
if hasattr(self.head, 'AMPA'):
if p['check']:
print("Setting pointer AMPA.U_SE_factor->RMECB.delta_U")
h.setpointer(self.head.AMPA._ref_U_SE_factor, 'delta_U', self.head.RMECB)
else:
raise Exception("RM_eCB mechanism require also AMPA")
if h.ismembrane('na_ion'):
self.head.ena = 55
if h.ismembrane('k_ion'):
self.head.ek = -90
# Access neck section
self.neck.push()
if h.ismembrane('na_ion'):
self.neck.ena = 55
if h.ismembrane('k_ion'):
self.neck.ek = -90
# Return to the origina section
h.pop_section()
h.pop_section()
if balance_currents:
self.head.balance_currents(p['Vrest'])
self.neck.balance_currents(p['Vrest'])
