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Added tests for the NEURON adapter (#65)
* neuron connection tests * 10 spikes for grc-sc * fixed imports
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,113 @@ | ||
| { | ||
| "name": "DBBS Mouse cerebellum configuration v4.0", | ||
| "output": { | ||
| "format": "scaffold.output.HDF5Formatter", | ||
| "file": "nrn_aa_goc.hdf5", | ||
| "morphology_repository": "morphologies.hdf5" | ||
| }, | ||
| "network_architecture": { | ||
| "simulation_volume_x": 150.0, | ||
| "simulation_volume_z": 150.0, | ||
| "store_kd_trees": true, | ||
| "store_compound_kd_tree": true, | ||
| "store_pf_kd_trees": true | ||
| }, | ||
| "layers": { | ||
| "test_layer": { | ||
| "thickness": 600, | ||
| "stack": { | ||
| "stack_id": 0, | ||
| "position_in_stack": 0, | ||
| "position": [0.0, 0.0, 0.0] | ||
| } | ||
| } | ||
| }, | ||
| "cell_types": { | ||
| "granule_cell": { | ||
| "placement": { | ||
| "class": "scaffold.placement.FixedPositions", | ||
| "layer": "test_layer", | ||
| "soma_radius": 2.5, | ||
| "count": 0, | ||
| "positions": [[0.0, 0.0, 0.0]] | ||
| }, | ||
| "morphology": { | ||
| "class": "scaffold.morphologies.NoGeometry" | ||
| }, | ||
| "plotting": { | ||
| "display_name": "lonely cell", | ||
| "color": "#E62214" | ||
| } | ||
| }, | ||
| "golgi_cell": { | ||
| "placement": { | ||
| "class": "scaffold.placement.FixedPositions", | ||
| "layer": "test_layer", | ||
| "soma_radius": 2.5, | ||
| "count": 0, | ||
| "positions": [[0.0, 0.0, 0.0]] | ||
| }, | ||
| "morphology": { | ||
| "class": "scaffold.morphologies.NoGeometry" | ||
| }, | ||
| "plotting": { | ||
| "display_name": "lonely cell", | ||
| "color": "#E62214" | ||
| } | ||
| } | ||
| }, | ||
| "connection_types": { | ||
| "granule_to_golgi": { | ||
| "class": "scaffold.connectivity.ConnectomeGlomerulusGranule", | ||
| "from_cell_types": [{"type": "granule_cell", "compartments": ["ascending_axon"]}], | ||
| "to_cell_types": [{"type": "golgi_cell", "compartments": ["basal_dendrites"]}], | ||
| "divergence": 50, | ||
| "convergence": 4 | ||
| } | ||
| }, | ||
| "simulations": { | ||
| "test": { | ||
| "simulator": "neuron", | ||
| "duration": 500, | ||
| "temperature": 32, | ||
| "resolution": 0.1, | ||
| "cell_models": { | ||
| "granule_cell": { | ||
| "model": "dbbs_models.GranuleCell", | ||
| "record_soma": true, | ||
| "record_spikes": true | ||
| }, | ||
| "golgi_cell": { | ||
| "model": "dbbs_models.GolgiCell", | ||
| "record_soma": true, | ||
| "record_spikes": true | ||
| } | ||
| }, | ||
| "connection_models": { | ||
| "granule_to_golgi": { | ||
| "synapse": ["AMPA", "NMDA"] | ||
| } | ||
| }, | ||
| "devices": { | ||
| "granule_stim": { | ||
| "io": "input", | ||
| "device": "current_clamp", | ||
| "targetting": "cell_type", | ||
| "cell_types": ["granule_cell"], | ||
| "parameters": { | ||
| "delay": 200, | ||
| "duration": 100, | ||
| "amplitude": 0.0105 | ||
| } | ||
| }, | ||
| "dendrite_recorders": { | ||
| "io": "output", | ||
| "device": "voltage_recorder", | ||
| "group": "dendrites", | ||
| "targetting": "representatives", | ||
| "section_type": "dendrites" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,113 @@ | ||
| { | ||
| "name": "DBBS Mouse cerebellum configuration v4.0", | ||
| "output": { | ||
| "format": "scaffold.output.HDF5Formatter", | ||
| "file": "nrn_aa_pc.hdf5", | ||
| "morphology_repository": "morphologies.hdf5" | ||
| }, | ||
| "network_architecture": { | ||
| "simulation_volume_x": 150.0, | ||
| "simulation_volume_z": 150.0, | ||
| "store_kd_trees": true, | ||
| "store_compound_kd_tree": true, | ||
| "store_pf_kd_trees": true | ||
| }, | ||
| "layers": { | ||
| "test_layer": { | ||
| "thickness": 600, | ||
| "stack": { | ||
| "stack_id": 0, | ||
| "position_in_stack": 0, | ||
| "position": [0.0, 0.0, 0.0] | ||
| } | ||
| } | ||
| }, | ||
| "cell_types": { | ||
| "granule_cell": { | ||
| "placement": { | ||
| "class": "scaffold.placement.FixedPositions", | ||
| "layer": "test_layer", | ||
| "soma_radius": 2.5, | ||
| "count": 0, | ||
| "positions": [[0.0, 0.0, 0.0]] | ||
| }, | ||
| "morphology": { | ||
| "class": "scaffold.morphologies.NoGeometry" | ||
| }, | ||
| "plotting": { | ||
| "display_name": "lonely cell", | ||
| "color": "#E62214" | ||
| } | ||
| }, | ||
| "purkinje_cell": { | ||
| "placement": { | ||
| "class": "scaffold.placement.FixedPositions", | ||
| "layer": "test_layer", | ||
| "soma_radius": 2.5, | ||
| "count": 0, | ||
| "positions": [[0.0, 0.0, 0.0]] | ||
| }, | ||
| "morphology": { | ||
| "class": "scaffold.morphologies.NoGeometry" | ||
| }, | ||
| "plotting": { | ||
| "display_name": "lonely cell", | ||
| "color": "#E62214" | ||
| } | ||
| } | ||
| }, | ||
| "connection_types": { | ||
| "granule_to_purkinje": { | ||
| "class": "scaffold.connectivity.ConnectomeGlomerulusGranule", | ||
| "from_cell_types": [{"type": "granule_cell", "compartments": ["ascending_axon"]}], | ||
| "to_cell_types": [{"type": "purkinje_cell", "compartments": ["apical_dendrites"]}], | ||
| "divergence": 50, | ||
| "convergence": 4 | ||
| } | ||
| }, | ||
| "simulations": { | ||
| "test": { | ||
| "simulator": "neuron", | ||
| "duration": 500, | ||
| "temperature": 32, | ||
| "resolution": 0.1, | ||
| "cell_models": { | ||
| "granule_cell": { | ||
| "model": "dbbs_models.GranuleCell", | ||
| "record_soma": true, | ||
| "record_spikes": true | ||
| }, | ||
| "purkinje_cell": { | ||
| "model": "dbbs_models.PurkinjeCell", | ||
| "record_soma": true, | ||
| "record_spikes": true | ||
| } | ||
| }, | ||
| "connection_models": { | ||
| "granule_to_purkinje": { | ||
| "synapse": ["AMPA_PF"] | ||
| } | ||
| }, | ||
| "devices": { | ||
| "granule_stim": { | ||
| "io": "input", | ||
| "device": "current_clamp", | ||
| "targetting": "cell_type", | ||
| "cell_types": ["granule_cell"], | ||
| "parameters": { | ||
| "delay": 200, | ||
| "duration": 100, | ||
| "amplitude": 0.0105 | ||
| } | ||
| }, | ||
| "dendrite_recorders": { | ||
| "io": "output", | ||
| "device": "voltage_recorder", | ||
| "group": "dendrites", | ||
| "targetting": "representatives", | ||
| "section_type": "dendrites" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,113 @@ | ||
| { | ||
| "name": "DBBS Mouse cerebellum configuration v4.0", | ||
| "output": { | ||
| "format": "scaffold.output.HDF5Formatter", | ||
| "file": "nrn_aa_goc.hdf5", | ||
| "morphology_repository": "morphologies.hdf5" | ||
| }, | ||
| "network_architecture": { | ||
| "simulation_volume_x": 150.0, | ||
| "simulation_volume_z": 150.0, | ||
| "store_kd_trees": true, | ||
| "store_compound_kd_tree": true, | ||
| "store_pf_kd_trees": true | ||
| }, | ||
| "layers": { | ||
| "test_layer": { | ||
| "thickness": 600, | ||
| "stack": { | ||
| "stack_id": 0, | ||
| "position_in_stack": 0, | ||
| "position": [0.0, 0.0, 0.0] | ||
| } | ||
| } | ||
| }, | ||
| "cell_types": { | ||
| "granule_cell": { | ||
| "placement": { | ||
| "class": "scaffold.placement.FixedPositions", | ||
| "layer": "test_layer", | ||
| "soma_radius": 2.5, | ||
| "count": 0, | ||
| "positions": [[0.0, 0.0, 0.0]] | ||
| }, | ||
| "morphology": { | ||
| "class": "scaffold.morphologies.NoGeometry" | ||
| }, | ||
| "plotting": { | ||
| "display_name": "lonely cell", | ||
| "color": "#E62214" | ||
| } | ||
| }, | ||
| "stellate_cell": { | ||
| "placement": { | ||
| "class": "scaffold.placement.FixedPositions", | ||
| "layer": "test_layer", | ||
| "soma_radius": 2.5, | ||
| "count": 0, | ||
| "positions": [[0.0, 0.0, 0.0]] | ||
| }, | ||
| "morphology": { | ||
| "class": "scaffold.morphologies.NoGeometry" | ||
| }, | ||
| "plotting": { | ||
| "display_name": "lonely cell", | ||
| "color": "#E62214" | ||
| } | ||
| } | ||
| }, | ||
| "connection_types": { | ||
| "granule_to_stellate": { | ||
| "class": "scaffold.connectivity.ConnectomeGlomerulusGranule", | ||
| "from_cell_types": [{"type": "granule_cell", "compartments": ["ascending_axon"]}], | ||
| "to_cell_types": [{"type": "stellate_cell", "compartments": ["basal_dendrites"]}], | ||
| "divergence": 50, | ||
| "convergence": 4 | ||
| } | ||
| }, | ||
| "simulations": { | ||
| "test": { | ||
| "simulator": "neuron", | ||
| "duration": 500, | ||
| "temperature": 32, | ||
| "resolution": 0.1, | ||
| "cell_models": { | ||
| "granule_cell": { | ||
| "model": "dbbs_models.GranuleCell", | ||
| "record_soma": true, | ||
| "record_spikes": true | ||
| }, | ||
| "stellate_cell": { | ||
| "model": "dbbs_models.StellateCell", | ||
| "record_soma": true, | ||
| "record_spikes": true | ||
| } | ||
| }, | ||
| "connection_models": { | ||
| "granule_to_stellate": { | ||
| "synapse": ["AMPA", "NMDA"] | ||
| } | ||
| }, | ||
| "devices": { | ||
| "granule_stim": { | ||
| "io": "input", | ||
| "device": "current_clamp", | ||
| "targetting": "cell_type", | ||
| "cell_types": ["granule_cell"], | ||
| "parameters": { | ||
| "delay": 200, | ||
| "duration": 100, | ||
| "amplitude": 0.021 | ||
| } | ||
| }, | ||
| "dendrite_recorders": { | ||
| "io": "output", | ||
| "device": "voltage_recorder", | ||
| "group": "dendrites", | ||
| "targetting": "representatives", | ||
| "section_type": "dendrites" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |
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