'morphology': 'Pvalb_469628681_m.swc',
'model_template': 'nml:Cell_473862421.cell.nml'
}]
point_models = [{
'model_name': 'LIF_exc',
'ei': 'e',
'dynamics_params': 'IntFire1_exc_1.json'
}, {
'model_name': 'LIF_inh',
'ei': 'i',
'dynamics_params': 'IntFire1_inh_1.json'
}]
morphologies = {
p['model_name']: SWCReader(
os.path.join('../biophys_components/morphologies', p['morphology']))
for p in bio_models
}
def build_edges(src,
trg,
sections=['basal', 'apical'],
dist_range=[50.0, 150.0]):
"""Function used to randomly assign a synaptic location based on the section (soma, basal, apical) and an
arc-length dist_range from the soma. This function should be passed into the network and called during the build
process.
:param src: source cell (dict)
:param trg: target cell (dict)
:param sections: list of target cell sections to synapse onto
'dynamics_params': 'NONE' if use_nml else 'json/473863035_fit.json'
}
]
cortex = NetworkBuilder("cortex")
for i, model_props in enumerate(cell_models):
cortex.add_nodes(N=3,
x=[i*30.0 + j for j in range(3)], y=[0.0]*3, z=[0.0]*3, # space cells every 10nm along x axs
model_type='biophysical',
model_processing='aibs_perisomatic',
**model_props)
cortex.build()
cortex.save_nodes(output_dir='network')
morphologies = {p['model_name']: SWCReader(os.path.join('../shared_components/morphologies', p['morphology']))
for p in cell_models}
def build_edges(src, trg, sections=['basal', 'apical'], dist_range=[50.0, 150.0]):
# Get morphology and soma center for the target cell
swc_reader = morphologies[trg['model_name']]
target_coords = [trg['x'], trg['y'], trg['z']]
sec_ids, sec_xs = swc_reader.choose_sections(sections, dist_range) # randomly choose sec_ids
coords = swc_reader.get_coord(sec_ids, sec_xs, soma_center=target_coords) # get coords of sec_ids
dist = swc_reader.get_dist(sec_ids)
swctype = swc_reader.get_type(sec_ids)
return sec_ids, sec_xs, coords[0][0], coords[0][1], coords[0][2], dist[0], swctype[0]
# Feedfoward excitatory virtual cells
'morphology': 'Nr5a1_471087815_m',
'model_template': 'nml:Cell_473863035.cell.nml'
},
{
'model_name': 'PV1', 'ei': 'i',
'morphology': 'Pvalb_470522102_m',
'model_template': 'nml:Cell_472912177.cell.nml'
},
{
'model_name': 'PV2', 'ei': 'i',
'morphology': 'Pvalb_469628681_m',
'model_template': 'nml:Cell_473862421.cell.nml'
}
]
morphologies = {p['model_name']: SWCReader(os.path.join('../shared_components/morphologies',
'{}.swc'.format(p['morphology'])))
for p in cell_models}
def build_edges(src, trg, sections=['basal', 'apical'], dist_range=[50.0, 150.0]):
"""Function used to randomly assign a synaptic location based on the section (soma, basal, apical) and an
arc-length dist_range from the soma. This function should be passed into the network and called during the build
process.
:param src: source cell (dict)
:param trg: target cell (dict)
:param sections: list of target cell sections to synapse onto
:param dist_range: range (distance from soma center) to place
:return:
"""
# Get morphology and soma center for the target cell
swc_reader = morphologies[trg['model_name']]
target_coords = [trg['x'], trg['y'], trg['z']]