data = pc.pyret()
# save file to folder
name = '{}_{}-{}_validation'.format(cell_type, data['meta']['round'],
data['meta']['id'])
cf.save_data(data, '{}/{}.json'.format(folder, name))
pc.done() # end parallelisation
# for timing simulations
print(
'Simulations completed (took %.0f secs).\nNow performing calculations/collating data...'
% (time.time() - start))
# ===== combine and/or average data =====
info = cf.params_for_input(cell_type, 'clustered')
clus_info = info['clustered']
# collates data loaded from files
data_all = {}
for i, iteration in enumerate(iterations):
round_data = {}
for r in range(n_rounds):
# load data
name = name = '{}_{}-{}_validation'.format(cell_type, r, iteration)
data = cf.load_data('{}/{}.json'.format(folder, name))
round_data[r] = data
# combine data
data_all[i] = round_data
raise ValueError(
"The requested cell type is not supported.\nOnly 'dpsn' and 'ispn' are recognised."
)
model_iterator = list(range(
specs[cell_type]
['N'])) # use model_iterator = range(specs[cell_type]['N']) for all models
# for dspn, 10 has lowest rheo, 54 has highest, 22 has mean, 41 has median; 22 is also average for experimental value
# for ispn, 8 has mean and median; 1 is average for experimental value
if pc.id() == 0:
print('Simulating {} cell iteration(s) of type: {}'.format(len(model_iterator),cell_type), \
flush=True)
# stimulation details
stim_info = cf.params_for_input(cell_type, 'clustered')
target = stim_info['clustered']['target']
target_labels = stim_info['clustered']['label']
stim_data = stim_info['clustered']['params']
# open library (channel distributions etc)
with open(specs[cell_type]['lib'], 'rb') as f:
model_sets = pickle.load(f, encoding="latin1")
# ===== simulate model(s) =====
data = {}
# model information to pass to simulations
model_data = {'specs':specs[cell_type], 'cell_type':cell_type, 'model_sets':model_sets, \
'target':target, 'target_labels':target_labels}
}
}
# chose cell type ('ispn' or 'dspn') and model id(s) to simulate...
cell_type = 'ispn' # 'dspn'/'ispn'
model_iterator = list(
range(specs[cell_type]['N'])
) # range(specs[cell_type]['N']) gives all models; must be a list for saving data!
# for dspn, 10 has lowest rheo, 54 has highest, 22 has mean, 41 has median; 22 is also average for experimental value
# for ispn, 8 has mean and median; 1 is average for experimental value
if pc.id() == 0:
print('Simulating {} cell(s) of type: {}'.format(len(model_iterator),
cell_type))
# stimulation details
stim_data = cf.params_for_input(cell_type, 'ACh')
# open library (channel distributions etc)
with open(specs[cell_type]['lib'], 'rb') as f:
model_sets = pickle.load(f, encoding="latin1")
# model information to pass to simulations
model_data = {
'specs': specs[cell_type],
'cell_type': cell_type,
'model_sets': model_sets
}
# ===== gets cholinergic modulation factors =====
mod_factors = cf.draw_factors_ACh(cell_type, mode='mean')
def dpp_generation(model_data,
cell_index,
run_info,
noise=True,
HFI=False,
HFI_delay=0,
dur_and_amp=True,
spike=False):
'''
Provides clustered glutamatergic input to SPNs to generate the dendritic
plateau potential in the absence of modulation.
INPUT(S):
- model_data: model paramaters (specification, cell type, model
sets, and stimulation targets) [dict]
- stim_data: stimulation parameters (number of inputs, time of inputs,
input inter-spike intervals, time to stop simulating) [dict]
- cell_index: cell specification being simulated [int]
- run_info: information about the simulation run (this simulation and
total number of simulations) [dict]
- dur_and_amp: whether to calculate the duration and peak amplitude of
the plateau potential (default True) [bool]
OUTPUT(S):
- data: simulated data including: simulation times; simulated voltages;
distance of stimulated target to the soma; rheobase of the model;
half-max width of the potential; peak amplitude of the potential;
cell specification being simulated; cell type being simulated
[dict]
- ncon: NetCon object
Thomas Binns (author), 26/01/21
'''
# ===== print simulation info to monitor progress =====
print('Simulating cell specification {} of {}'.format( \
run_info['curr_n']+1,run_info['tot_n']),flush = True)
# ===== gets stimulation info =====
# clustered inputs
clus_info = cf.params_for_input(model_data['cell_type'], 'clustered')
clus_params = clus_info['clustered']['params']
# noise inputs
if noise:
noise_info = cf.params_for_input(model_data['cell_type'], 'noise')
noise_params = noise_info['noise']['params']
# HFIs
if HFI:
HFI_info = cf.params_for_input(model_data['cell_type'], 'HFI')
HFI_params = HFI_info['HFI']['params']
# ===== simulation =====
data = {}
for i, tar in enumerate(
clus_info['clustered']['target']): # for each simulation target
clus_lab = clus_info['clustered']['label'][i] # label for input target
# initiate cell
cell = build.MSN(
params=model_data['specs']['par'],
morphology=model_data['specs']['morph'],
variables=model_data['model_sets'][cell_index]['variables'])
rheobase = model_data['model_sets'][cell_index]['rheobase']
# record vectors
tm = h.Vector()
tm.record(h._ref_t)
vm = h.Vector()
vm.record(cell.soma(0.5)._ref_v)
# add clustered inputs
clus_syn, clus_stim, clus_ncon, clus_d2soma = cf.set_clustered_stim(
cell,
tar,
n=clus_params['stim_n'],
act_time=clus_params['stim_t'],
ISI=clus_params['isi'])
# add background noise
if noise:
'''
noise_syn, noise_stim, noise_ncon = cf.set_noise(cell, model_data['cell_type'],
freq_glut=noise_params['freq_glut'], freq_gaba=noise_params['freq_gaba'],
n_glut=noise_params['n_glut'], n_gaba=noise_params['n_gaba'], only_dend=noise_params['only dend'],
glut_delay=noise_params['stim_t'], gaba_delay=noise_params['stim_t'])
'''
noise_syn, noise_stim, noise_ncon = cf.set_bg_noise(
cell,
model_data['cell_type'],
fglut=noise_params['freq_glut'],
fgaba=noise_params['freq_gaba'],
dendOnly=noise_params['only dend'])
# add high-frequency inputs
if HFI:
# adds HFI
HFI_syn, HFI_stim, HFI_ncon, arrangement = cf.set_HFI(
cell,
model_data['cell_type'],
freq=HFI_params['freq'],
n_inputs=HFI_params['n_inputs'],
delay=clus_params['stim_t'] +
(clus_params['stim_n'] * clus_params['isi']) + HFI_delay,
exclude=HFI_info['HFI']['exclude'])
# collates data
data['HFI'] = arrangement
# run simulation
h.finitialize(-80)
while h.t < clus_params['stop_t'] + HFI_delay + (
clus_params['stim_n'] * clus_params['isi']):
h.fadvance()
tm = tm.to_python()
vm = vm.to_python()
# collate data
data[clus_lab] = {'vm': vm}
data['meta'] = {
'id': int(cell_index),
'round': run_info['round'],
'cell_type': model_data['cell_type'],
'tm': tm,
'rheo': rheobase
}
# calculate dpp duration and amplitude
if dur_and_amp:
base_t_start = tm.index(
min(tm,
key=lambda x: abs(x - (clus_params['stim_t'] + clus_params[
'pre_t']))))
base_t_end = tm.index(
min(tm, key=lambda x: abs(x - clus_params['stim_t'])))
base_vm = np.mean(vm[base_t_start:base_t_end])
data[clus_lab]['dur'] = cf.dpp_dur(tm, vm, base_vm,
clus_params['stim_t'])
data[clus_lab]['amp'] = cf.dpp_amp(tm, vm, base_vm,
clus_params['stim_t'])
# get spike-related data
if spike:
spiked = 0
thresh = 0
# checks whether spike occured
data[clus_lab]['spiked'] = 0
if max(vm) > thresh:
data[clus_lab]['spiked'] = 1
spiked = 1
# checks time of first spike number of spikes that occured (if any)
data[clus_lab]['first_spike'] = []
data[clus_lab]['spike_n'] = []
if spiked == 1:
data[clus_lab]['first_spike'] = tm[next(
i for i, x in enumerate(vm) if x > 0)]
data[clus_lab]['spike_n'] = cf.spike_n(vm)
return data
def dpp_DA_modded(model_data,
cell_index,
run_info,
noise=True,
HFI=False,
HFI_delay=0,
dur_and_amp=True,
spike=False,
mod_tar='all'):
'''
Provides clustered glutamatergic input to SPNs to generate the dendritic
plateau potential in the absence of modulation.
INPUT(S):
- model_data: model paramaters (specification, cell type, model
sets, and stimulation targets) [dict]
- stim_data: stimulation parameters (number of inputs, time of inputs,
input inter-spike intervals, time to stop simulating) [dict]
- cell_index: cell specification being simulated [int]
- run_info: information about the simulation run (this simulation and
total number of simulations) [dict]
- dur_and_amp: whether to calculate the duration and peak amplitude of
the plateau potential (default True) [bool]
OUTPUT(S):
- data: simulated data including: simulation times; simulated voltages;
distance of stimulated target to the soma; rheobase of the model;
half-max width of the potential; peak amplitude of the potential;
cell specification being simulated; cell type being simulated
[dict]
- ncon: NetCon object
Thomas Binns (author), 13/02/21
'''
# ===== print simulation info to monitor progress =====
print('Simulating cell specification {} of {}'.format( \
run_info['curr_n']+1,run_info['tot_n']),flush = True)
# ===== gets stimulation info =====
# clustered inputs
clus_info = cf.params_for_input(model_data['cell_type'], 'clustered')
clus_params = clus_info['clustered']['params']
# modulation inputs
mod_factors = cf.draw_factors_DA(model_data['cell_type'], mode='random')
DA_info = cf.params_for_input(model_data['cell_type'], 'DA')
DA_params = DA_info['DA']['params']
# gets vector for modulation timing
state = [1 if ht >= DA_params['stim_t'] and ht <= DA_params['stop_t'] \
else 0 for ht in np.arange(0,clus_params['stop_t'],h.dt)]
state = h.Vector(state)
# collates time-dependent mechanism modulation scaling
mech_scale = {}
for key in mod_factors:
mech_scale[key] = state
# noise inputs
if noise:
noise_info = cf.params_for_input(model_data['cell_type'], 'noise')
noise_params = noise_info['noise']['params']
# HFIs
if HFI:
HFI_info = cf.params_for_input(model_data['cell_type'], 'HFI')
HFI_params = HFI_info['HFI']['params']
# ===== simulation =====
data = {}
for i, clus_tar in enumerate(
clus_info['clustered']['target']): # for each simulation target
clus_lab = clus_info['clustered']['label'][i] # label for input target
data[clus_lab] = {}
# get the targets for cholinergic input
DA_targets = {}
DA_targets['target'] = [clus_tar]
DA_targets['label'] = [clus_lab]
for j, DA_t in enumerate(DA_info['DA']['target']):
DA_targets['target'].append(DA_t)
DA_targets['label'].append(DA_info['DA']['label'][j])
target_x = .5
if mod_tar == 'all':
DA_targets['target'] = ['all']
DA_targets['label'] = ['all']
target_x = 'all'
for j, DA_t in enumerate(
DA_targets['target']): # for each cholinergic input target
DA_lab = DA_targets['label'][j]
# initiate cell
cell = build.MSN(
params=model_data['specs']['par'],
morphology=model_data['specs']['morph'],
variables=model_data['model_sets'][cell_index]['variables'])
rheobase = model_data['model_sets'][cell_index]['rheobase']
# record vectors
tm = h.Vector()
tm.record(h._ref_t)
vm = h.Vector()
vm.record(cell.soma(0.5)._ref_v)
# add clustered inputs
clus_syn, clus_stim, clus_ncon, clus_d2soma = cf.set_clustered_stim(
cell,
clus_tar,
n=clus_params['stim_n'],
act_time=clus_params['stim_t'],
ISI=clus_params['isi'])
# add background noise
if noise:
noise_syn, noise_stim, noise_ncon = cf.set_bg_noise(
cell,
model_data['cell_type'],
fglut=noise_params['freq_glut'],
fgaba=noise_params['freq_gaba'],
dendOnly=noise_params['only dend'])
# add high-frequency inputs
if HFI:
# adds HFI
HFI_syn, HFI_stim, HFI_ncon, arrangement = cf.set_HFI(
cell,
model_data['cell_type'],
freq=HFI_params['freq'],
n_inputs=HFI_params['n_inputs'],
delay=clus_params['stim_t'] +
(clus_params['stim_n'] * clus_params['isi']) + HFI_delay,
exclude=HFI_info['HFI']['exclude'])
# collates data
data['HFI'] = arrangement
# get cholinergic modulation class
modulation = modulate.set_DA(cell,
mod_factors, [DA_t],
target_x=target_x,
play=mech_scale,
dt=h.dt)
# run simulation
h.finitialize(-80)
while h.t < clus_params['stop_t'] + HFI_delay + (
clus_params['stim_n'] * clus_params['isi']):
h.fadvance()
tm = tm.to_python()
vm = vm.to_python()
# collate data
data[clus_lab][DA_lab] = {'vm': vm}
data['meta'] = {
'id': int(cell_index),
'round': run_info['round'],
'cell_type': model_data['cell_type'],
'tm': tm,
'rheo': rheobase
}
# calculate dpp duration and amplitude
if dur_and_amp:
base_t_start = tm.index(
min(tm,
key=lambda x: abs(x - (clus_params['stim_t'] +
clus_params['pre_t']))))
base_t_end = tm.index(
min(tm, key=lambda x: abs(x - clus_params['stim_t'])))
base_vm = np.mean(vm[base_t_start:base_t_end])
data[clus_lab][DA_lab]['dur'] = cf.dpp_dur(
tm, vm, base_vm, clus_params['stim_t'])
data[clus_lab][DA_lab]['amp'] = cf.dpp_amp(
tm, vm, base_vm, clus_params['stim_t'])
# get spike-related data
if spike:
thresh = 0
# checks whether spike occured
data[clus_lab][DA_lab]['spiked'] = 0
if max(vm) > thresh:
data[clus_lab][DA_lab]['spiked'] = 1
return data
import neuron as nrn
import MSN_builder as build
import pickle
import common_functions as cf
import numpy as np
from neuron import h
from matplotlib import pyplot as plt
from matplotlib.colors import LinearSegmentedColormap as lsc
# what to visualise =============
cell_type = input("What cell type should be visualised: dspn; or ispn?")
input_type = input(
"What input should be visualised: 'clustered'; 'HFI'; or 'ACh'?")
vis_info = cf.params_for_input(cell_type, input_type)
# sets up cell =============
#nrn.load_mechanisms('mechanisms/single')
h.load_file('stdlib.hoc')
h.load_file('import3d.hoc')
# specs
specs = {
'dspn': {
'N': 71,
'lib': 'Libraries/D1_71bestFit_updRheob.pkl',
'par': 'Params/params_dMSN.json',
'morph': 'Morphologies/WT-dMSN_P270-20_1.02_SGA1-m24.swc'
},