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3.6.0b6 - Restored functionality of casali_2019 config
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@Helveg
Helveg committed Dec 9, 2020
1 parent 2b6562d commit 609aa77
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Showing 4 changed files with 34 additions and 154 deletions.
2 changes: 1 addition & 1 deletion bsb/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
__version__ = "3.6.0b5"
__version__ = "3.6.0b6"

from .reporting import set_verbosity, report, warn
167 changes: 27 additions & 140 deletions bsb/configurations/casali_2019.json
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,19 @@
}
},
"cell_types": {
"mossy_fibers": {
"entity": true,
"relay": true,
"placement": {
"class": "bsb.placement.Entities",
"layer": "granular_layer",
"placement_relative_to": "glomerulus",
"placement_count_ratio": 0.05
},
"plotting": {
"color": "black"
}
},
"granule_cell": {
"placement": {
"class": "bsb.placement.LayeredRandomWalk",
Expand Down Expand Up @@ -172,6 +185,11 @@
}
},
"connection_types": {
"mossy_to_glomerulus": {
"class": "bsb.connectivity.ConnectomeMossyGlomerulus",
"from_cell_types": [{"type": "mossy_fibers", "compartments": ["soma"]}],
"to_cell_types": [{"type": "glomerulus", "compartments": ["soma"]}]
},
"glomerulus_to_granule": {
"class": "bsb.connectivity.ConnectomeGlomerulusGranule",
"from_cell_types": [{"type": "glomerulus", "compartments": ["soma"]}],
Expand All @@ -186,13 +204,6 @@
"divergence": 40,
"convergence": 4
},
"glomerulus_to_dcn": {
"class": "bsb.connectivity.ConnectomeGlomDCN",
"from_cell_types": [{"type": "glomerulus", "compartments": ["soma"]}],
"to_cell_types": [{"type": "dcn_cell", "compartments": ["dendrites"]}],
"divergence": 147,
"convergence": 2
},
"granule_to_golgi": {
"class": "bsb.connectivity.ConnectomeGranuleGolgi",
"from_cell_types": [{"type": "granule_cell", "compartments": ["parallel_fiber", "ascending_axon"]}],
Expand Down Expand Up @@ -438,58 +449,6 @@
"k2": 0.047,
"A1": 13.857,
"A2":3.477}
},
"dcn_interneuron": {
"parameters": {
"t_ref": 3.02,
"C_m": 55.0,
"V_th": -39.0,
"V_reset": -69.0,
"E_L": -40.0
},
"iaf_cond_alpha": {
"I_e": 55.75,
"tau_syn_ex": 7.1,
"tau_syn_in": 13.6,
"g_L": 1.56
},
"eglif_cond_alpha_multisyn": {
"Vinit": -40.0,
"lambda":0.9,
"deltaV":1.0,
"tau_m": 56.0,
"I_e": 2.384,
"k_adap": 0.079,
"k1": 0.041,
"k2": 0.044,
"A1": 176.358,
"A2":176.358}
},
"io_cell": {
"parameters": {
"t_ref": 3.7,
"C_m": 189.0,
"V_th": -35.0,
"V_reset": -45.0,
"E_L": -45.0
},
"iaf_cond_alpha": {
"I_e": 55.75,
"tau_syn_ex": 1.0,
"tau_syn_in": 60.0,
"g_L": 1.56
},
"eglif_cond_alpha_multisyn": {
"Vinit": -45.0,
"lambda":1.2,
"deltaV":0.8,
"tau_m": 11.0,
"I_e": -10.101,
"k_adap": 1.928,
"k1": 0.191,
"k2": 0.091,
"A1": 1810.923,
"A2":1358.197}
}
},
"connection_models": {
Expand Down Expand Up @@ -654,85 +613,13 @@
"Wmax": 100.0
}
}
},
"glomerulus_to_dcn": {
"plastic": false,
"hetero": false,
"teaching": "purkinje_to_dcn",
"connection": {
"weight":0.0006,
"delay": 4.0
},
"synapse": {
"static_synapse": {},
"stdp_synapse_cosexp": {
"A_minus": 0.5,
"A_plus": 0.05,
"Wmin": 0.0,
"Wmax": 100.0
}
}
},
"io_to_purkinje": {
"connection": {
"weight":-2.0,
"delay": 1.0
},
"synapse": {
"static_synapse": {}
}
},
"io_to_basket": {
"connection": {
"weight":-2.0,
"delay": 1.0
},
"synapse": {
"static_synapse": {}
}
},
"io_to_stellate": {
"connection": {
"weight":-2.0,
"delay": 1.0
},
"synapse": {
"static_synapse": {}
}
},
"io_to_dcn": {
"connection": {
"weight":-2.0,
"delay": 1.0
},
"synapse": {
"static_synapse": {}
}
},
"io_to_dcn_interneuron": {
"connection": {
"weight":-2.0,
"delay": 1.0
},
"synapse": {
"static_synapse": {}
}
},
"dcn_interneuron_to_io": {
"connection": {
"weight":-2.0,
"delay": 1.0
},
"synapse": {
"static_synapse": {}
}
}
},
"devices": {
"background_stimulation": {
"device": "poisson_generator",
"io": "input",
"type": "cell_type",
"targetting": "cell_type",
"cell_types": ["glomerulus"],
"parameters": {
"rate": 1.0,
Expand All @@ -743,7 +630,7 @@
"center_stimulation": {
"device": "spike_generator",
"io": "input",
"type": "local",
"targetting": "local",
"radius": 70.0,
"origin": [200.0, 675.0, 200.0],
"cell_types": ["glomerulus"],
Expand All @@ -761,7 +648,7 @@
"record_glomerulus_spikes": {
"device": "spike_detector",
"io": "output",
"type": "cell_type",
"targetting": "cell_type",
"cell_types": ["glomerulus"],
"parameters": {
"withgid": true,
Expand All @@ -773,7 +660,7 @@
"record_granule_spikes": {
"device": "spike_detector",
"io": "output",
"type": "cell_type",
"targetting": "cell_type",
"cell_types": ["granule_cell"],
"parameters": {
"withgid": true,
Expand All @@ -785,7 +672,7 @@
"record_golgi_spikes": {
"device": "spike_detector",
"io": "output",
"type": "cell_type",
"targetting": "cell_type",
"cell_types": ["golgi_cell"],
"parameters": {
"withgid": true,
Expand All @@ -797,7 +684,7 @@
"record_purkinje_spikes": {
"device": "spike_detector",
"io": "output",
"type": "cell_type",
"targetting": "cell_type",
"cell_types": ["purkinje_cell"],
"parameters": {
"withgid": true,
Expand All @@ -809,7 +696,7 @@
"record_stellate_spikes": {
"device": "spike_detector",
"io": "output",
"type": "cell_type",
"targetting": "cell_type",
"cell_types": ["stellate_cell"],
"parameters": {
"withgid": true,
Expand All @@ -821,7 +708,7 @@
"record_basket_spikes": {
"device": "spike_detector",
"io": "output",
"type": "cell_type",
"targetting": "cell_type",
"cell_types": ["basket_cell"],
"parameters": {
"withgid": true,
Expand All @@ -833,7 +720,7 @@
"record_dcn_spikes": {
"device": "spike_detector",
"io": "output",
"type": "cell_type",
"targetting": "cell_type",
"cell_types": ["dcn_cell"],
"parameters": {
"withgid": true,
Expand Down
1 change: 0 additions & 1 deletion bsb/connectivity/connectome/granule_golgi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,6 @@ def connect(self):
n_connAA = self.aa_convergence
n_conn_pf = self.pf_convergence
tot_conn = n_connAA + n_conn_pf
pf_heights = self.scaffold.appends["cells/ascending_axon_lengths"]

def connectome_grc_goc(
first_granule,
Expand Down
18 changes: 6 additions & 12 deletions bsb/connectivity/connectome/pf_interneuron.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,26 +18,20 @@ def connect(self):
interneurons = self.scaffold.cells_by_type[interneuron_cell_type.name]
first_granule = int(granules[0, 0])
dendrite_radius = interneuron_cell_type.morphology.dendrite_radius
pf_heights = (
self.scaffold.appends["cells/ascending_axon_lengths"][:, 1] + granules[:, 3]
) # Add granule Y to height of its pf
# Spoof fixed pf height of 150 µm
pf_heights = 150 + granules[:, 3]

def connectome_pf_inter(first_granule, interneurons, granules, r_sb, h_pf):
pf_interneuron = np.zeros((0, 2))

for (
i
) in (
interneurons
): # for each interneuron find all the parallel fibers that fall into the sphere with centre the cell soma and appropriate radius
# for each interneuron find all the parallel fibers that fall into the sphere with centre the cell soma and appropriate radius
for i in interneurons:

# find all cells that satisfy the condition
interneuron_matrix = (
((granules[:, 2] - i[2]) ** 2) + ((h_pf - i[3]) ** 2) - (r_sb ** 2)
).__le__(0)
good_pf = np.where(interneuron_matrix)[
0
] # indexes of interneurons that can potentially be connected
# indexes of interneurons that can potentially be connected
good_pf = np.where(interneuron_matrix)[0]

matrix = np.zeros((len(good_pf), 2))
matrix[:, 1] = i[0]
Expand Down

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