def get_cell(output_folder, do_simulation=True):
def insert_synapses(synparams, section, n, spTimesFun, args):
# find n compartments to insert synapses onto
# idx = [clamp_1['idx'], clamp_2['idx']]#
idx = cell.get_rand_idx_area_norm(section=section, nidx=n)
# spiketimes = [np.array([15, 25]), np.array([16,26])]
# Insert synapses in an iterative fashion
for count, index in enumerate(idx):
synparams.update({"idx": int(index)})
s = LFPy.Synapse(cell, **synparams)
spiketimes = spTimesFun(args[0], args[1], args[2], args[3])
s.set_spike_times(spiketimes)
# s.set_spike_times(spiketimes[count])
cell = LFPy.Cell(**cellParameters)
cell.set_rotation(x=-pl.pi / 2)
cell.set_rotation(y=pl.pi / 2)
# find_sec_from_comp(cell, 756)
cell.set_pos(xpos=-25)
# cell.set_rotation(x = pl.pi/2)
# cell.set_rotation(y = -pl.pi/2)
# cell.set_rotation(y = pl.pi/10)
cell.set_rotation(z=-pl.pi / 165)
# find_sec_from_comp(cell, 644)
# find_sec_from_comp(cell, 801)
# plot_sec(cell, 'apic[76]')
# sys.exit()
def insert_glutamate_stim(cell, section="apic[63]", site=0.5):
gmaxS = 10
neuron.h("access %s" % section)
glut_syn = neuron.h.glutamate(site)
glut_syn.delay = 50
glut_syn.ntar = 1.3
glut_syn.gmax = gmaxS
glut_syn.Nspike = 3
glut_syn.Tspike = 20
return glut_syn
def insert_many_glutamate_stim(cell, nSyn=500):
import random
gmaxS = 1
syn_array = []
i = 0
while i < nSyn:
apic_sec = random.randint(0, 108)
section = "apic[%d]" % apic_sec
comps = cell.get_idx_section(section)
idx = random.choice(comps)
if cell.ymid[idx] > 600:
# syns_positions.append(
neuron.h("access %s" % section)
syn_array.append(neuron.h.glutamate(random.uniform(0.1, 0.95)))
syn_array[-1].delay = 50
syn_array[-1].ntar = 1
syn_array[-1].gmax = gmaxS
syn_array[-1].Nspike = 3
syn_array[-1].Tspike = 20
i += 1
return syn_array # , syns_positions
if do_simulation:
os.system("cp %s %s" % (sys.argv[0], output_folder))
np.save(output_folder + "x_start.npy", cell.xstart)
np.save(output_folder + "y_start.npy", cell.ystart)
np.save(output_folder + "z_start.npy", cell.zstart)
np.save(output_folder + "x_end.npy", cell.xend)
np.save(output_folder + "y_end.npy", cell.yend)
np.save(output_folder + "z_end.npy", cell.zend)
np.save(output_folder + "diam.npy", cell.diam)
syn1 = insert_glutamate_stim(cell, section=find_sec_from_comp(cell, 615), site=0.5)
syn2 = insert_glutamate_stim(cell, section=find_sec_from_comp(cell, 646), site=0.59)
syn3 = insert_glutamate_stim(cell, section=find_sec_from_comp(cell, 671), site=0.5)
syn4 = insert_glutamate_stim(cell, section=find_sec_from_comp(cell, 623), site=0.2)
syn5 = insert_glutamate_stim(cell, section=find_sec_from_comp(cell, 628), site=0.9)
syn6 = insert_glutamate_stim(cell, section=find_sec_from_comp(cell, 657), site=0.8)
# currentClamp_1 = LFPy.StimIntElectrode(cell, **clamp_1)
# currentClamp_2 = LFPy.StimIntElectrode(cell, **clamp_2)
# insert_synapses(synapseParameters_AMPA, **insert_synapses_AMPA_args)
# insert_synapses(synapseParameters_NMDA, **insert_synapses_NMDA_args)
# insert_synapses(synapseParameters_GABA_A, **insert_synapses_GABA_A_args)
# syn_array = insert_many_glutamate_stim(cell, nSyn = 100)
# neuron.h('objref n_vec')
# neuron.h('n_vec = new Vector()')
# neuron.h('n_vec.record(&soma.m_hh(0.5))')
cell.simulate(**simulationParameters)
np.save(output_folder + "imem.npy", cell.imem)
np.save(output_folder + "vmem.npy", cell.vmem)
np.save(output_folder + "tvec.npy", cell.tvec)
plotstuff(cell, clamp_1, clamp_2)
os.system("cp %s %s" % ("example_fig.png", output_folder))
else:
cell.vmem = np.load(output_folder + "vmem.npy")
cell.imem = np.load(output_folder + "imem.npy")
cell.tvec = np.load(output_folder + "tvec.npy")
return cell
def get_cell(output_folder, do_simulation = True):
def insert_synapses(synparams, name, section, n, spTimesFun, args):
#find n compartments to insert synapses onto
#idx = [clamp_1['idx'], clamp_2['idx']]#
idx = cell.get_rand_idx_area_norm(section=section, nidx=n)
#if name == 'NMDA':
# idx_tuft = []
# for i in idx:
# if cell.zmid[i] > 500:
# idx_tuft.append(i)
# idx = idx_tuft
#spiketimes = [np.array([15, 25]), np.array([16,26])]
#Insert synapses in an iterative fashion
for count, i in enumerate(idx):
synparams.update({'idx' : int(i)})
s = LFPy.Synapse(cell,**synparams)
spiketimes = spTimesFun(args[0], args[1], args[2], args[3])
s.set_spike_times(spiketimes)
#s.set_spike_times(spiketimes[count])
def insert_glutamate_stim(cell, section = 'apic[63]', site = 0.5):
gmaxS=20
neuron.h('access %s' %section)
glut_syn = neuron.h.glutamate(site)
glut_syn.delay = 50
glut_syn.ntar = 1
glut_syn.gmax = gmaxS
glut_syn.Nspike=2
glut_syn.Tspike=20
return glut_syn
def insert_many_glutamate_stim(cell, nSyn = 500):
import random
gmaxS=1
syn_array = []
i = 0
while i < nSyn:
apic_sec = random.randint(0,115)
section = 'apic[%d]' % apic_sec
comps = cell.get_idx_section(section)
idx = random.choice(comps)
if cell.ymid[idx] > 800:
#syns_positions.append(
neuron.h('access %s' % section)
syn_array.append(neuron.h.glutamate(random.uniform(0.5,0.95)))
syn_array[-1].delay = 50
syn_array[-1].ntar = 1
syn_array[-1].gmax = gmaxS
syn_array[-1].Nspike=3
syn_array[-1].Tspike=20
i += 1
return syn_array#, syns_positions
cell = LFPy.Cell(**cellParameters)
cell.apic_11 = cell.get_closest_idx(x=52.52, y=441.92, z=0.75)
cell.apic_58 = cell.get_closest_idx(x=29.05, y=742.84, z=-34.05)
cell.apic_59 = cell.get_closest_idx(x = 20.9, y = 825.51, z = -40.25)
cell.set_pos(xpos = -45)
cell.set_rotation(y = -pl.pi/2)
cell.set_rotation(y = pl.pi/10)
cell.set_rotation(z = +pl.pi/65)
if do_simulation:
os.system('cp %s %s' %(sys.argv[0], output_folder))
np.save(output_folder + 'x_start.npy', cell.xstart)
np.save(output_folder + 'y_start.npy', cell.ystart)
np.save(output_folder + 'z_start.npy', cell.zstart)
np.save(output_folder + 'x_end.npy', cell.xend)
np.save(output_folder + 'y_end.npy', cell.yend)
np.save(output_folder + 'z_end.npy', cell.zend)
np.save(output_folder + 'diam.npy', cell.diam)
try:
np.save(output_folder + 'ica.npy',cell.rec_variables['ica'])
np.save(output_folder + 'cai.npy',cell.rec_variables['cai'])
except:
pass
#currentClamp_1 = LFPy.StimIntElectrode(cell, **clamp_1)
#currentClamp_2 = LFPy.StimIntElectrode(cell, **clamp_2)
#currentClamp_3 = LFPy.StimIntElectrode(cell, **clamp_3)
#insert_synapses(synapseParameters_AMPA, **insert_synapses_AMPA_args)
#insert_synapses(synapseParameters_NMDA, **insert_synapses_NMDA_args)
#insert_synapses(synapseParameters_GABA_A, **insert_synapses_GABA_A_args)
#glut_syn = insert_glutamate_stim(cell, section = 'apic[63]')
#glut_syn2 = insert_glutamate_stim(cell, section = 'apic[45]')
#glut_syn = insert_many_glutamate_stim(cell, 100)
#glut_syn1 = insert_glutamate_stim(cell, section = 'apic[63]', site = 0.59)
#glut_syn2 = insert_glutamate_stim(cell, section = 'apic[71]', site = 0.59)
#glut_syn3 = insert_glutamate_stim(cell, section = 'apic[71]', site = 0.31)
cell.simulate(**simulationParameters)
np.save(output_folder + 'imem.npy', cell.imem)
np.save(output_folder + 'vmem.npy', cell.vmem)
np.save(output_folder + 'tvec.npy', cell.tvec)
plotstuff(cell, clamp_1, clamp_2)
os.system('cp %s %s' %('example_fig.png', output_folder))
else:
cell.vmem = np.load(output_folder + 'vmem.npy')
cell.imem = np.load(output_folder + 'imem.npy')
cell.tvec = np.load(output_folder + 'tvec.npy')
try:
cell.rec_variables['ica'] = np.load(output_folder + 'ica.npy')
cell.rec_variables['cai'] = np.load(output_folder + 'cai.npy')
except:
pass
return cell