def __init__(self, name=None):
self.mk_soma(name='soma', diam=10, L=20)
self.mk_dendrite(3,
dend_name='short_1',
sec_names=['proxd', 'midd', 'distd'],
diam=[3, 2, 1],
L=[50, 50, 50],
soma_loc=0.0)
self.mk_dendrite(3,
dend_name='short_2',
sec_names=['proxd', 'midd', 'distd'],
diam=[3, 2, 1],
L=[50, 50, 50],
soma_loc=0.0)
self.mk_dendrite(3,
dend_name='long_1',
sec_names=['proxd', 'midd', 'distd'],
diam=[3, 2, 1],
L=[75, 75, 75],
soma_loc=1.0)
self.mk_dendrite(3,
dend_name='long_2',
sec_names=['proxd', 'midd', 'distd'],
diam=[3, 2, 1],
L=[75, 75, 75],
soma_loc=1.0)
parameters = params.read_parameters('hippcellparams.txt')
self.parameters = parameters
self.insert_mechs(parameters)
def __init__(self, name=None):
# Make soma
self.mk_soma(name='soma', diam=15, L=20)
# Make dendrites
self.mk_dendrite(4,
dend_name='basal_1',
sec_names=['proxd', 'mid1', 'mid2', 'ddend'],
diam=[4, 3, 2, 1],
L=[50, 50, 50, 50],
soma_loc=0)
self.mk_dendrite(4,
dend_name='basal_2',
sec_names=['proxd', 'mid1', 'mid2', 'ddend'],
diam=[4, 3, 2, 1],
L=[50, 50, 50, 50],
soma_loc=0)
self.mk_dendrite(4,
dend_name='apical_1',
sec_names=['proxd', 'mid1', 'mid2', 'ddend'],
diam=[4, 3, 2, 1],
L=[75, 75, 75, 75],
soma_loc=1.0)
self.mk_dendrite(4,
dend_name='apical_2',
sec_names=['proxd', 'mid1', 'mid2', 'ddend'],
diam=[4, 3, 2, 1],
L=[75, 75, 75, 75],
soma_loc=1.0)
dirname = os.path.dirname(__file__)
filepath = os.path.join(dirname, 'basketcellparams.txt')
parameters = params.read_parameters(filepath)
self.insert_mechs(parameters)
def __init__(self, name=None):
self.name = name
self.all_secs = []
self.dendrites = []
self.mk_soma(name='soma', diam=20, L=20)
# Set up the sections with topology
"""NOTE! There is a discrepancy here between the diameter of the third
section of the dendrite. Publication: 25; Code: 2.5 The number in
the code seems to be more physiological"""
self.mk_dendrite(4,
dend_name='dend_1',
sec_names=['proxd', 'mid1d', 'mid2d', 'dd'],
diam=[5.78, 4, 2.5, 1],
L=[50, 50, 50, 50],
soma_loc=1)
self.mk_dendrite(4,
dend_name='dend_2',
sec_names=['proxd', 'mid1d', 'mid2d', 'dd'],
diam=[5.78, 4, 2.5, 1],
L=[50, 50, 50, 50],
soma_loc=1)
self.mk_dendrite(4,
dend_name='dend_3',
sec_names=['proxd', 'mid1d', 'mid2d', 'dd'],
diam=[5.78, 4, 2.5, 1],
L=[50, 50, 50, 50],
soma_loc=0)
self.mk_dendrite(4,
dend_name='dend_4',
sec_names=['proxd', 'mid1d', 'mid2d', 'dd'],
diam=[5.78, 4, 2.5, 1],
L=[50, 50, 50, 50],
soma_loc=0)
# Difference between mossycell and mossycell_cat.
# mossycell_cat imports mossycellparams_cat.txt
dirname = os.path.dirname(__file__)
filepath = os.path.join(dirname, 'mossycellparams_cat.txt')
parameters = params.read_parameters(filepath)
self.insert_mechs(parameters)
def __init__(self):
self.mk_soma(name='soma', diam=20, L=16.8)
# Make dendrites
self.mk_dendrite(4,
dend_name='dend_1',
sec_names=['gcld', 'proxd', 'midd', 'dd'],
diam=[5, 4, 3, 2],
L=[50.0, 150.0, 150.0, 150.0],
soma_loc=0)
self.mk_dendrite(4,
dend_name='dend_2',
sec_names=['gcld', 'proxd', 'midd', 'dd'],
diam=[5, 4, 3, 2],
L=[50.0, 150.0, 150.0, 150.0],
soma_loc=1)
parameters = params.read_parameters('testneuronparams.txt')
self.insert_mechs(parameters)
def __init__(self, name=None):
# Make soma
self.mk_soma(name='soma', diam=16.8, L=16.8)
# Make dendrites
self.mk_dendrite(4,
dend_name='dend_1',
sec_names=['gcld', 'proxd', 'midd', 'dd'],
diam=[3.0, 3.0, 3.0, 3.0],
L=[50.0, 150.0, 150.0, 150.0],
soma_loc=1.0)
self.mk_dendrite(4,
dend_name='dend_2',
sec_names=['gcld', 'proxd', 'midd', 'dd'],
diam=[3.0, 3.0, 3.0, 3.0],
L=[50.0, 150.0, 150.0, 150.0],
soma_loc=1.0)
dirname = os.path.dirname(__file__)
filepath = os.path.join(dirname, 'granulecellparams.txt')
parameters = params.read_parameters(filepath)
self.insert_mechs(parameters)