bmtk.simulator.bionet.default_setters package¶
Submodules¶
bmtk.simulator.bionet.default_setters.cell_models module¶
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bmtk.simulator.bionet.default_setters.cell_models.
Biophys1
(cell, template_name, dynamic_params)[source]¶ Loads a biophysical NEURON hoc object using Cell-Types database objects.
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bmtk.simulator.bionet.default_setters.cell_models.
Biophys1_dict
(cell)[source]¶ Set parameters for cells from the Allen Cell Types database Prior to setting parameters will replace the axon with the stub
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bmtk.simulator.bionet.default_setters.cell_models.
IntFire1
(cell, template_name, dynamics_params)[source]¶ Loads a point integrate and fire neuron
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bmtk.simulator.bionet.default_setters.cell_models.
NMLLoad
(cell, template_name, dynamic_params)[source]¶ Convert a NEUROML file to a NEURON hoc cell object.
Current limitations: * Ignores nml morphology section. You must pass in a swc file * Only for biophysically detailed cell biophysical components. All properties must be assigned to a segment group.
Parameters: - cell –
- template_name –
- dynamic_params –
Returns:
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bmtk.simulator.bionet.default_setters.cell_models.
aibs_allactive
(hobj, cell, dynamics_params)[source]¶
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bmtk.simulator.bionet.default_setters.cell_models.
aibs_allactive_directed
(hobj, cell, dynamics_params)[source]¶
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bmtk.simulator.bionet.default_setters.cell_models.
aibs_perisomatic
(hobj, cell, dynamics_params)[source]¶
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bmtk.simulator.bionet.default_setters.cell_models.
aibs_perisomatic_directed
(hobj, cell, dynamics_params)[source]¶
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bmtk.simulator.bionet.default_setters.cell_models.
fix_axon_allactive
(hobj)[source]¶ Replace reconstructed axon with a stub
Parameters: - hobj: instance of a Biophysical template
NEURON’s cell object
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bmtk.simulator.bionet.default_setters.cell_models.
fix_axon_peri
(hobj)[source]¶ Replace reconstructed axon with a stub
Parameters: hobj – hoc object
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bmtk.simulator.bionet.default_setters.cell_models.
loadHOC
(cell, template_name, dynamics_params)[source]¶
bmtk.simulator.bionet.default_setters.synapse_models module¶
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bmtk.simulator.bionet.default_setters.synapse_models.
Exp2Syn
(syn_params, sec_x, sec_id)[source]¶ Create a list of exp2syn synapses
Parameters: - syn_params – parameters of a synapse
- sec_x – normalized distance along the section
- sec_id – target section
Returns: NEURON synapse object
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bmtk.simulator.bionet.default_setters.synapse_models.
exp2syn
(syn_params, xs, secs)[source]¶ Create a list of exp2syn synapses
Parameters: - syn_params – parameters of a synapse
- xs – list of normalized distances along the section
- secs – target sections
Returns: list of NEURON synpase objects
bmtk.simulator.bionet.default_setters.synaptic_weights module¶
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bmtk.simulator.bionet.default_setters.synaptic_weights.
default_weight_fnc
(edge_props, src_props, trg_props)[source]¶