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Cell models update #29

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Merged
filimarc merged 16 commits into from
Oct 9, 2025
Merged

Cell models update #29

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193951d
morpho updated: scaled tag (-10), adjusted links to soma
danilobenozzo Nov 6, 2024
f8821e0
update model files: GrC, GC, PC
danilobenozzo Nov 6, 2024
9f8ba8d
changed name: XXCellModel, XXCellModel.swc_tags
danilobenozzo Nov 6, 2024
d447ed9
stellate and basket models
danilobenozzo Nov 14, 2024
c9373b8
updated BC conf file and morphos SC and BC
rizland Dec 19, 2024
f017f43
updated name Cav mod
rizland Dec 19, 2024
6437982
update basket
rizland Jan 29, 2025
ae149fd
swapped yz BC SC
danilobenozzo Jan 30, 2025
f933278
black basket conf file
danilobenozzo Jan 30, 2025
e7f132d
soma children attached to closest point
danilobenozzo Jan 31, 2025
d34b594
set basket cell AIS length 29.9
danilobenozzo Feb 6, 2025
3e30547
renamed gmax GABA syn, basketcell Nav1_6 set to 0.25
danilobenozzo Feb 6, 2025
a21bc6b
gap mech in golgi cell
danilobenozzo Feb 27, 2025
dc76e38
updated syn params
danilobenozzo Feb 27, 2025
711d056
typo BS GABAsyn
danilobenozzo Mar 13, 2025
08e1935
added mech Iext in PC
danilobenozzo Mar 19, 2025
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105 changes: 60 additions & 45 deletions dbbs_models/basket_cell_models.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,26 +4,35 @@
{
"synapse_types": {
"AMPA": {
"tau_facil": 54,
"tau_rec": 35.1,
"tau_1": 6,
"gmax": 1200,
"U": 0.4,
"mechanism": "AMPA",
"parameters": {
"tau_facil": 10.8,
"tau_rec": 35.1,
"tau_1": 10,
"gmax": 1200,
"U": 0.13,
},
},
("NMDA", "stellate"): {
"tau_facil": 5,
"tau_rec": 8,
"tau_1": 1,
"gmax": 5000,
"U": 0.15,
"NMDA": {
"mechanism": ("NMDA", "stellate"),
"parameters": {
"tau_facil": 10.8,
"tau_rec": 35.1,
"tau_1": 10,
"gmax": 5000,
"U": 0.13,
},
},
"GABA": {
"tau_facil": 0,
"tau_rec": 38.7,
"tau_1": 1,
"gmax": 3200,
"U": 0.42,
"Erev": -65,
"mechanism": "GABA",
"parameters": {
"tau_facil": 0,
"tau_rec": 38.7,
"tau_1": 1,
"gmaxA1": 3200,
"U": 0.42,
"Erev": -65,
},
},
},
"cable_types": {
Expand All @@ -36,28 +45,30 @@
"h": {"rev_pot": -34},
},
"mechanisms": {
"Leak": {"e": -60, "gmax": 3e-05},
"Nav1_1": {"gbar": 0.10946415489712},
"Cav3_2": {"gcabar": 0.0006295539},
"Cav3_3": {"pcabar": 0.0007543986},
# "CaL13": {"pcaLbar": 0.0002593795},
"Kir2_3": {"gkbar": 0.0012770833},
"Kv3_4": {"gkbar": 0.0277114781},
"Kca1_1": {"gbar": 0.0044251081},
"Cav2_1": {"pcabar": 0.000846789},
"HCN1": {"gbar": 0.0006902196},
"cdp5": {"TotalPump": 1e-09},
"Leak": {"e": -55, "gmax": 0.00004},
"Nav1_1": {"gbar": 0.2},
"Cav3_2": {"gcabar": 0.0001},
"Cav1_2": {"gbar": 0.0007},
"Cav1_3": {"gbar": 5e-06},
"Kir2_3": {"gkbar": 0.0001},
"Kv3_4": {"gkbar": 0.097},
"Kv4_3": {"gkbar": 0.01},
"Kca3_1": {"gkbar": 0.001},
"HCN1": {"gbar": 0.001},
"cdp5": {"TotalPump": 2e-09},
},
},
"dendrites": {
"cable": {"Ra": 122, "cm": 1},
"ions": {"k": {"rev_pot": -80}},
"mechanisms": {
"Leak": {"e": -60, "gmax": 3e-05},
"Cav2_1": {"pcabar": 0.0004965596},
"Kca1_1": {"gbar": 0.0020575902},
"Kv1_1": {"gbar": 0.0285137286},
"cdp5": {"TotalPump": 1e-09},
"Leak": {"e": -55, "gmax": 1e-05},
"Cav3_2": {"gcabar": 0.00005},
"Cav1_2": {"gbar": 0.0002},
"Cav1_3": {"gbar": 5e-06},
"Kv4_3": {"gkbar": 0.00987201764943},
"Kca2_2": {"gkbar": 0.0065},
"cdp5": {"TotalPump": 2e-09},
},
},
"axon": {
Expand All @@ -68,12 +79,14 @@
"h": {"rev_pot": -34},
},
"mechanisms": {
"Leak": {"e": -60, "gmax": 3e-05},
"Kv1_1": {"gbar": 0.0069654709},
"Nav1_6": {"gbar": 0.0072983226},
"Kv3_4": {"gkbar": 0.0151487764},
"HCN1": {"gbar": 0.0034633208},
"cdp5": {},
"Leak": {"e": -55, "gmax": 1e-06},
"Kv1_1": {"gbar": 0.0005},
"Nav1_6": {"gbar": 0.001},
"Kv3_4": {"gkbar": 0.001},
"HCN1": {"gbar": 0.0001},
"Kca1_1": {"gbar": 0.001},
"Cav2_1": {"pcabar": 0.00008},
"cdp5": {"TotalPump": 1e-09},
},
},
"axon_initial_segment": {
Expand All @@ -84,12 +97,14 @@
"h": {"rev_pot": -34},
},
"mechanisms": {
"Leak": {"e": -60, "gmax": 3e-05},
"HCN1": {"gbar": 0.0048096086},
"Nav1_6": {"gbar": 0.5724695612},
"Kv1_1": {"gbar": 0.0827297077},
"Kv3_4": {"gkbar": 0.0300388404},
"cdp5": {},
"Leak": {"e": -55, "gmax": 1e-05},
"HCN1": {"gbar": 0.001},
"Nav1_6": {"gbar": 0.25},
"Kv1_1": {"gbar": 0.02333516534870},
"Kv3_4": {"gkbar": 0.002},
"Kca1_1": {"gbar": 0.01},
"Cav2_1": {"pcabar": 2.2e-4},
"cdp5": {"TotalPump": 1e-09},
},
},
},
Expand Down
132 changes: 106 additions & 26 deletions dbbs_models/golgi_cell_models.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,37 +3,59 @@
GolgiCellModel = define_model(
{
"synapse_types": {
"AMPA": {
"tau_facil": 54,
"tau_rec": 35.1,
"tau_1": 30,
"gmax": 1200,
"U": 0.4,
"AMPA_PF": {
"mechanism": "AMPA",
"parameters": {
"tau_facil": 54,
"tau_rec": 35.1,
"tau_1": 30,
"gmax": 1200,
"U": 0.4,
},
},
"AMPA_AA": {
"mechanism": "AMPA",
"parameters": {
"tau_facil": 54,
"tau_rec": 35.1,
"tau_1": 30,
"gmax": 1200,
"U": 0.4,
},
},
"AMPA": {
"tau_facil": 54,
"tau_rec": 35.1,
"tau_1": 30,
"gmax": 1200,
"U": 0.4,
"AMPA_MF": {
"mechanism": ("AMPA", "granule"),
"parameters": {
"tau_facil": 8,
"tau_rec": 5,
"tau_1": 1,
"gmax": 1200,
"U": 0.43,
},
},
("NMDA", "stellate"): {
"tau_facil": 5,
"tau_rec": 8,
"tau_1": 1,
"gmax": 10000,
"U": 0.43,
"NMDA": {
"mechanism": ("NMDA", "stellate"),
"parameters": {
"tau_facil": 5,
"tau_rec": 8,
"tau_1": 1,
"gmax": 10000,
"U": 0.43,
},
},
"GABA": {
"tau_facil": 0,
"tau_rec": 38.7,
"tau_1": 1,
"gmax": 3200,
"U": 0.42,
"Erev": -65,
"mechanism": "GABA",
"parameters": {
"tau_facil": 0,
"tau_rec": 38.7,
"tau_1": 1,
"gmaxA1": 3200,
"U": 0.42,
"Erev": -65,
},
},
# "gap_s": {"point_process": "gap_junction", "source": "vgap"},
# "gap": {"point_process": ("gap_junction", "parallel"), "source": "vgap"},
"gap_s": {"mechanism": "gap_junction", "source": "vgap"},
"gap": {"mechanism": ("gap_junction", "parallel"), "source": "vgap"},
},
"cable_types": {
"soma": {
Expand Down Expand Up @@ -72,6 +94,52 @@
"Ca": {"gcabar": 0.00139885617712},
("cdp5", "CAM_GoC"): {"TotalPump": 2e-09},
},
"synapses": {
"AMPA_PF": {
"mechanism": "AMPA",
"parameters": {
"tau_facil": 54,
"tau_rec": 35.1,
"tau_1": 30,
"gmax": 1200,
"U": 0.4,
},
},
"AMPA_AA": {
"mechanism": "AMPA",
"parameters": {
"tau_facil": 54,
"tau_rec": 35.1,
"tau_1": 30,
"gmax": 1200,
"U": 0.4,
},
},
"AMPA_MF": {
"mechanism": ("AMPA", "granule"),
},
"NMDA": {
"mechanism": ("NMDA", "stellate"),
"parameters": {
"tau_facil": 5,
"tau_rec": 8,
"tau_1": 1,
"gmax": 10000,
"U": 0.43,
},
},
"GABA": {
"mechanism": "GABA",
"parameters": {
"tau_facil": 0,
"tau_rec": 38.7,
"tau_1": 1,
"gmaxA1": 3200,
"U": 0.42,
"Erev": -65,
},
},
},
},
"apical_dendrites": {
"cable": {"Ra": 122, "cm": 2.5},
Expand All @@ -89,6 +157,18 @@
"Cav3_1": {"pcabar": 3.690771983e-05},
("cdp5", "CAM_GoC"): {"TotalPump": 5e-09},
},
"synapses": {
"AMPA_PF": {
"mechanism": "AMPA",
"parameters": {
"tau_facil": 54,
"tau_rec": 35.1,
"tau_1": 30,
"gmax": 1200,
"U": 0.4,
},
},
},
},
"axon": {
"cable": {"Ra": 122, "cm": 1},
Expand Down
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