def add_cpampars(self,
locations,
section_name,
release_time,
gmax=500,
pconc=100):
for section in self.dendrites:
if section.name() == section_name:
self.dendrite = section
#print 'adding synapses to', self.dendrite.name()
pre = h.Section()
pre.diam = 1.0
pre.L = 1.0
pre.insert('rel')
pre.dur_rel = 0.5
pre.amp_rel = 1.0
pre.del_rel = release_time
self.pre_cpampa_list.append(pre)
for loc in locations:
cpampa = h.cpampa12st(loc, sec=self.dendrite)
cpampa.pconc = pconc
cpampa.gmax = gmax
h.setpointer(pre(0.5).rel._ref_T, 'C', cpampa)
self.cpampa_list.append(cpampa)
def get_synapse_iv(self,
synpase_type='ampa',
p_conc=0,
ampa_gmax=5000,
nmda_gmax=5000,
t_rel=40.0,
vc_range=np.arange(-90.0, 50.0, 5.0),
nmda_mech='h.NMDA_Mg_T',
vshift=None):
'''
Method for generating large IV curves... Not sure if best, use synapse __ref__i
'''
self.clamp = h.SEClamp(0.5, sec=self.root)
self.clamp.dur1 = 10
self.clamp.dur2 = 60
self.clamp.dur3 = 10
self.clamp.amp1 = -70
self.clamp.amp2 = -70
self.clamp.amp3 = -70
self.clamp.rs = 0.0001
pre = h.Section()
pre.diam = 1.0
pre.L = 1.0
pre.insert('rel')
pre.dur_rel = 0.5
pre.amp_rel = 3.0
pre.del_rel = t_rel
if synpase_type.lower() == 'ampa':
print('running simulation of AMPAR IV with', p_conc,
'µM polyamines')
cpampa = h.cpampa12st(0.5, sec=self.root)
cpampa.pconc = p_conc
cpampa.gmax = ampa_gmax
h.setpointer(pre(0.5).rel._ref_T, 'C', cpampa)
if synpase_type.lower() == 'nmda':
print('running simulation of NMDA IV')
nmda = eval(nmda_mech + '(0.5,sec=self.root)')
print('inserted: ' + nmda_mech + '(0.5,sec=self.root)')
#nmda = h.NMDA_Mg_T(0.5,sec=self.root)
if vshift:
print('vshift: ' + str(vshift))
nmda.vshift = vshift
nmda.gmax = nmda_gmax
h.setpointer(pre(0.5).rel._ref_T, 'C', nmda)
v, i, t = self.run_vclamp(vc_range, tstop=80)
i_list, v_list = self.calc_iv_relationship(v, i, t)
return i_list, v_list,
def add_cpampa(self, pconc=100, gmax=1000, release_time=50):
syn = h.cpampa12st(0.5, sec=self.soma)
syn.pconc = pconc
syn.gmax = gmax
pre = h.Section()
pre.diam = 1.0
pre.L = 1.0
pre.insert('rel')
pre.dur_rel = 0.5
pre.amp_rel = 2.0
pre.del_rel = release_time
h.setpointer(pre(0.5).rel._ref_T, 'C', syn)
self.syn = syn
self.pre = pre
def get_iv(self,
synpase_type='ampa',
p_conc=0,
ampa_gmax=5000,
nmda_gmax=5000,
t_rel=40.0):
self.clamp = h.SEClamp(0.5, sec=self.root)
self.clamp.dur1 = 10
self.clamp.dur2 = 60
self.clamp.dur3 = 10
self.clamp.amp1 = -70
self.clamp.amp2 = -70
self.clamp.amp3 = -70
self.clamp.rs = 0.0001
pre = h.Section()
pre.diam = 1.0
pre.L = 1.0
pre.insert('rel')
pre.dur_rel = 0.5
pre.amp_rel = 3.0
pre.del_rel = t_rel
if synpase_type.lower() == 'ampa':
print('running simulation of AMPAR IV with', p_conc,
'µM polyamines')
cpampa = h.cpampa12st(0.5, sec=self.root)
cpampa.pconc = p_conc
cpampa.gmax = ampa_gmax
h.setpointer(pre(0.5).rel._ref_T, 'C', cpampa)
if synpase_type.lower() == 'nmda':
print('running simulation of NMDA IV')
nmda = h.NMDA_Mg_T(0.5, sec=self.root)
nmda.gmax = nmda_gmax
h.setpointer(pre(0.5).rel._ref_T, 'C', nmda)
vc_range = np.arange(-90.0, 50.0, 10.0)
v, i, t = self.run_vclamp(vc_range, tstop=80)
i_list, v_list = self.calc_iv_relationship(v, i, t)
return i_list, v_list
def get_nmda_ampa_ratio(self,
p_conc,
ampa_gmax,
nmda_gmax,
t_rel=40.0,
vc_range=[-60, 60]):
self.clamp = h.SEClamp(0.5, sec=self.root)
self.clamp.dur1 = 10
self.clamp.dur2 = 150
self.clamp.dur3 = 10
self.clamp.amp1 = -70
self.clamp.amp2 = -70
self.clamp.amp3 = -70
self.clamp.rs = 0.0001
pre = h.Section()
pre.diam = 1.0
pre.L = 1.0
pre.insert('rel')
pre.dur_rel = 0.5
pre.amp_rel = 3.0
pre.del_rel = t_rel
syn_list = []
locs = np.linspace(0, 1, 35)
for l in locs:
cpampa = h.cpampa12st(l, sec=self.root)
cpampa.pconc = p_conc
cpampa.gmax = ampa_gmax
h.setpointer(pre(0.5).rel._ref_T, 'C', cpampa)
nmda = h.NMDA_Mg_T(l, sec=self.root)
nmda.gmax = nmda_gmax
h.setpointer(pre(0.5).rel._ref_T, 'C', nmda)
syn_list.append((nmda, cpampa))
v, i, t = self.run_vclamp(vc_range, tstop=170)
return v, i, t
def add_cpampars_for_stim_electrodes(self,
section_loc_list,
release_time,
stim_string,
gmax=500,
pconc=100):
'''
Method adds across sections, expects a list of tuples containing (section(str), loc(float)).
Stores the stims in a dictionary...
'''
# should make this a method
pre = h.Section()
pre.diam = 1.0
pre.L = 1.0
pre.insert('rel')
pre.dur_rel = 0.5
pre.amp_rel = 1.0
pre.del_rel = release_time
self.pre_cpampa_list.append(pre)
stim_syns = []
for sec_loc in section_loc_list:
section_name = sec_loc[0]
loc = sec_loc[1]
#print 'adding at:', section_name, loc
for section in self.dendrites:
if section.name() == section_name:
dendrite = section
cpampa = h.cpampa12st(loc, sec=dendrite)
cpampa.pconc = pconc
cpampa.gmax = gmax
h.setpointer(pre(0.5).rel._ref_T, 'C', cpampa)
stim_syns.append(cpampa)
self.cpampa_stim_dict[stim_string] = stim_syns
# hacky just go with last dendrite for recording - change this!
self.dendrite = dendrite
def add_cpampars(self,
locations,
dendrite_strings,
gmax=500,
release_times=[20],
pconc=100,
NMDARs=False):
self.cpampa_list = []
self.pre_cpampa_list = []
self.NMDARs_list = []
# find the dendrite of choice!
for string in dendrite_strings:
for sec in self.sec_list:
if sec.name().find(string) >= 0:
self.dendrite = sec
for x, loc in enumerate(locations):
pre = h.Section()
pre.diam = 1.0
pre.L = 1.0
pre.insert('rel')
pre.dur_rel = 0.5
pre.amp_rel = 1.0
pre.del_rel = release_times[x]
cpampa = h.cpampa12st(locations[x], sec=self.dendrite)
cpampa.pconc = pconc
cpampa.gmax = gmax
if NMDARs:
NMDA = h.NMDA_Mg_T(locations[x], sec=self.dendrite)
NMDA.gmax = gmax
h.setpointer(pre(0.5).rel._ref_T, 'C', NMDA)
self.NMDARs_list.append(NMDA)
h.setpointer(pre(0.5).rel._ref_T, 'C', cpampa)
self.cpampa_list.append(cpampa)
self.pre_cpampa_list.append(pre)
def get_ampa_iv_2017(self,
ampa_gmax,
p_conc=0,
vc_range=[-60, 60],
tstop=220,
t_rel=40.0):
self.clamp = h.SEClamp(0.5, sec=self.root)
self.clamp.dur1 = 10
self.clamp.dur2 = 200
self.clamp.dur3 = 10
self.clamp.amp1 = -70
self.clamp.amp2 = -70
self.clamp.amp3 = -70
self.clamp.rs = 0.0001
pre = h.Section()
pre.diam = 1.0
pre.L = 1.0
pre.insert('rel')
pre.dur_rel = 0.5
pre.amp_rel = 3.0
pre.del_rel = t_rel
print('amp 3')
cpampa = h.cpampa12st(0.5, sec=self.root)
cpampa.pconc = p_conc
cpampa.gmax = ampa_gmax
h.setpointer(pre(0.5).rel._ref_T, 'C', cpampa)
h.load_file('stdrun.hoc')
rec = {}
for label in 't', 'v', 'i_ampa', 'g_ampa':
rec[label] = h.Vector()
rec['t'].record(h._ref_t)
rec['i_ampa'].record(cpampa._ref_i)
rec['g_ampa'].record(cpampa._ref_g)
rec['v'].record(self.root(0.5)._ref_v)
v_list, i_list, t_list, g_list = [], [], [], []
h.tstop = tstop
h.celsius = 32.0
for vc in vc_range:
h.init()
#h.finitialize(v_init)
self.clamp.amp2 = vc
h.run()
i = rec['i_ampa'].to_python()
g = rec['g_ampa'].to_python()
v = rec['v'].to_python()
t = rec['t'].to_python()
v_list.append(v)
i_list.append(i)
t_list.append(t)
g_list.append(g)
v = np.array(v_list).transpose()
i = np.array(i_list).transpose() * 1000 # for pA
t = np.array(t_list).transpose()
g = np.array(g_list).transpose(
) * 1 * 10**6 # this is defined as microSiemens in the mod file: 1000000, so for pico 1e-6
return t, i, v, g # in pA
def add_uncaging_spots(self,
random_seed=7,
n_synapses=15,
uncaging_dendrite='jc_tree2_bdend1[2]',
ampa_gmax=500,
nmda_gmax=500,
rel_time=20,
delay=0.5,
pconc=100,
nmda=False,
spots='all',
loc_range=(0, 1),
wipe_lists=True):
# grab dendrite
for section in self.sec_list:
if section.name() == uncaging_dendrite:
self.u_dend = section
# do these neeed to be here?
if wipe_lists:
self.cpampa_list = []
self.nmda_list = []
self.pre_list = []
##
locs = np.linspace(loc_range[0], loc_range[1], n_synapses)
np.random.seed(random_seed)
possible_locs = np.random.permutation(locs)
release_times = np.array(
[rel_time + delay * i for i in range(n_synapses)])
if spots == 'all':
print('uncaging on all spots:')
uncaging_spots = possible_locs
else:
uncaging_spots = possible_locs[spots]
release_times = release_times[spots]
for i, loc in enumerate(uncaging_spots):
pre = h.Section()
pre.diam = 1.0
pre.L = 1.0
pre.insert('rel')
pre.dur_rel = 0.5
pre.amp_rel = 3.0
pre.del_rel = release_times[i]
cpampa = h.cpampa12st(loc, sec=self.u_dend)
cpampa.pconc = pconc
cpampa.gmax = ampa_gmax
h.setpointer(pre(0.5).rel._ref_T, 'C', cpampa)
self.cpampa_list.append(cpampa)
self.pre_list.append(pre)
if nmda:
nmda = h.NMDA_Mg_T(loc, sec=self.u_dend)
nmda.gmax = nmda_gmax
h.setpointer(pre(0.5).rel._ref_T, 'C', nmda)
self.nmda_list.append(nmda)