def setUpClass(cls):
cls.cell = SpineCell(name="cell")
cls.soma = cls.cell.add_sec("soma", add_pas=True, nseg=10)
cls.cell._add_spines_to_section(cls.soma,
"new",
0.5,
1,
1,
0.5,
0.5,
None,
None,
None,
None,
add_pas=False)
cls.head = cls.cell.heads[0]
cls.neck = cls.cell.necks[0]
cls.cell2 = SpineCell(name="cell2")
cls.soma2 = cls.cell2.add_sec("soma", nseg=10, add_pas=True)
cls.cell2._add_spines_to_section(cls.soma2,
"new",
0.3,
.5,
.5,
0.3,
0.3,
None,
None,
None,
None,
add_pas=True)
cls.head2 = cls.cell2.heads[0]
cls.neck2 = cls.cell2.necks[0]
cls.cell3 = SpineCell(name="cell3")
cls.soma3 = cls.cell3.add_sec("soma", add_pas=True)
cls.cell3._add_spines_to_section(cls.soma3, "new", 0.3, .5, .5, 0.3,
0.3, -80, 1 / 30000, 100, 2)
cls.head3 = cls.cell3.heads[0]
cls.neck3 = cls.cell3.necks[0]
cls.cell4 = SpineCell(name="cell4")
cls.soma4 = cls.cell4.add_sec("soma", add_pas=True)
cls.cell4._add_spines_to_section(cls.soma4, "new",
[0.1, 0.2, 0.4, 0.8], .5, .5, 0.4,
0.4, -80, 1 / 40000, 100, 2)
cls.head4 = cls.cell4.heads
cls.neck4 = cls.cell4.necks
def setUpClass(cls):
path = os.path.dirname(os.path.abspath(__file__))
f_path = os.path.join(path, "..", "commons/mods/combe2018")
cls.cell = SpineCell("cell", compile_paths=f_path)
cls.soma = cls.cell.add_sec("soma", add_pas=True, nseg=10)
cls.soma.hoc.insert("hh")
diam = 5
lengths = [10]
cls.dends = []
for i, length in enumerate(lengths):
dend = cls.cell.add_sec("dend%d" % i,
add_pas=True,
nseg=int(length / 10),
l=length,
diam=diam)
cls.dends.append(dend)
if i == 0:
cls.cell.connect_secs(dend, cls.soma)
else:
cls.cell.connect_secs(dend, cls.dends[i - 1])
cls.gbar_dend = 0.0002
cls.gbar_spine = 0.0001
cls.gkca = 0.00075
cls.cell.insert("calH", "dend", gcalbar=cls.gbar_dend)
cls.cell.insert("kca", "dend", gbar=cls.gkca)
cls.regions = cls.cell.filter_secs("dend", as_list=True)
cls.cell.add_spines_by_density(cls.regions,
0.02,
"thin",
add_pas=True,
spine_cm=10)
cls.cell.insert("calH", "head", gcalbar=cls.gbar_spine)
cls.cell.compensate(cm_adjustment=False, calH="gcalbar")
cls.cell.compensate(cm_adjustment=False, kca="gbar")
cls.cell.compensate(cm_adjustment=True)
def setUpClass(cls):
path = os.path.dirname(os.path.abspath(__file__))
f_path = os.path.join(path, "..", "commons/mods/combe2018")
cls.cell = SpineCell("cell", compile_paths=f_path)
cls.soma = cls.cell.add_sec("soma", add_pas=True, nseg=10)
cls.diam = 5
cls.lengths = np.linspace(100, 50, 5)
cls.dends = []
for i, length in enumerate(cls.lengths):
dend = cls.cell.add_sec("dend%d" % i,
add_pas=True,
nseg=int(length / 10),
l=length,
diam=cls.diam)
cls.dends.append(dend)
if i == 0:
cls.cell.connect_secs(dend, cls.soma)
else:
cls.cell.connect_secs(dend, cls.dends[i - 1])
cls.regions = cls.cell.filter_secs("dend", as_list=True)
cls.cell.add_spines_by_density(cls.regions, 0.02, "thin", add_pas=True)
cls.cell.insert("calH", cls.cell.heads, gcalbar=0.0001)
cls.out_calH = cls.cell._get_spine_factor(cls.cell.spines[:2], "calH",
"gcalbar")
cls.out_cm = cls.cell._get_spine_factor(cls.cell.spines[:2], "cm",
None)
def setUpClass(cls):
path = os.path.dirname(os.path.abspath(__file__))
f_path = os.path.join(path, "..", "commons/mods/combe2018")
cls.cell = SpineCell("cell", compile_paths=f_path)
cls.soma = cls.cell.add_sec("soma", add_pas=True, nseg=10)
cls.soma.hoc.insert("hh")
diam = 5
lengths = np.linspace(100, 50, 10)
cls.dends = []
for i, length in enumerate(lengths):
dend = cls.cell.add_sec("dend%d" % i,
add_pas=True,
nseg=int(length / 10),
l=length)
cls.dends.append(dend)
if i == 0:
cls.cell.connect_secs(dend, cls.soma)
else:
cls.cell.connect_secs(dend, cls.dends[i - 1])
cls.cell.insert("calH", "dend", gcalbar=0.0002)
cls.cell.insert("kca", "dend", gbar=0.00075)
cls.regions = cls.cell.filter_secs("dend", as_list=True)
cls.cell.add_spines_by_density(cls.regions, 0.02, "thin", add_pas=True)
cls.cell.insert("calH", "head", gcalbar=0.0001)
cls.find_calH = cls.cell.get_spines_by_section("calH")
cls.find_kca = cls.cell.get_spines_by_section("kca")
cls.find_all = cls.cell.get_spines_by_section(None)
def setUpClass(cls):
cell = SpineCell(name="cell")
cls.soma = cell.add_sec("soma", g_pas=1 / 30000, E_rest=-76,
ra=40, cm=1.1, nseg=100, add_pas=True)
cls.e_pas1, cls.g_pas1, cls.ra1, \
cls.cm1 = establish_electric_properties(cls.soma,
None, None,
None, None)
cls.e_pas2, cls.g_pas2, cls.ra2, \
cls.cm2 = establish_electric_properties(cls.soma,
-79, 1 / 20000,
50, 1.2)
cls.dend = cell.add_sec("dend")
cls.e_pas3, cls.g_pas3, cls.ra3, \
cls.cm3 = establish_electric_properties(cls.dend, None, None,
None, None)
def setUpClass(cls):
cls.cell1 = SpineCell(name="cell1")
cls.dend1 = cls.cell1.add_sec("dend1", add_pas=True)
cls.dend2 = cls.cell1.add_sec("dend2", add_pas=True)
cls.cell1.connect_secs(cls.dend2, cls.dend1)
cls.spine_density = 2 / 100
cls.n_spines = 2
cls.head_diam = cls.head_len = 1
cls.neck_diam = cls.neck_len = 0.5
cls.E_pas = -80
cls.g_pas = 1 / 20000
cls.ra = 100
cls.cm = 1.1
cls.out_1 = cls.cell1.add_spines_to_section_list(
[cls.dend1, cls.dend2],
cls.spine_density,
spine_type="mushroom",
spine_E_pas=cls.E_pas,
spine_g_pas=cls.g_pas,
spine_ra=cls.ra,
spine_cm=cls.cm,
u_random=None,
area_density=False,
add_pas=True)
cls.cell2 = SpineCell(name="cell2")
cls.dend21 = cls.cell2.add_sec("dend1", add_pas=True)
cls.dend22 = cls.cell2.add_sec("dend2", add_pas=True)
cls.cell2.connect_secs(cls.dend21, cls.dend22)
cls.out_2 = cls.cell2.add_spines_to_section_list(
[cls.dend21, cls.dend22],
cls.spine_density,
spine_type="mushroom",
head_diam=cls.head_diam,
head_len=cls.head_len,
neck_diam=cls.neck_diam,
neck_len=cls.neck_len,
add_pas=False,
u_random=1,
area_density=False)
cls.cell3 = SpineCell(name="cell3")
cls.soma3 = cls.cell3.add_sec("soma", add_pas=False)
cls.cell3.add_spines_to_section_list([cls.soma3],
cls.spine_density,
spine_type="weird",
add_pas=False)
def __init__(self, name=None, compile_paths=None):
SpineCell.__init__(self, name, compile_paths=compile_paths)
SynapticGroupCell.__init__(self, name, compile_paths=compile_paths)
def __init__(self, name=None, compile_paths=None):
ComplexSynapticCell.__init__(self, name, compile_paths=compile_paths)
SpineCell.__init__(self, name)
def setUpClass(cls):
cell = SpineCell(name="cell")
cls.soma = cell.add_sec("soma", nseg=10)