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Retinal Stimulation Modeling Environment
  • Retinal Stimulation Modeling Environment (RSME)
  • Preliminaries
    • Python
    • NEURON
    • Systems Biology Markup Language
    • RSME and Model initialization
  • Model specification
    • Meta-parameters
    • Morphology Description
    • Network Description
    • Visual Stimulation
    • Biophysical Description
  • Visual Stimulation
  • Single SAC model
    • Model Initialization
    • Model Visualization
    • Model Simulation
  • SAC plexus model
    • Before we begin
    • Model Initialization and Visualization
    • Model Simulation
  • SAC-DSGC network
    • Model initialization and visualization
    • Model Simulation
  • Logger
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  1. SAC plexus model

Model Initialization and Visualization

PreviousBefore we beginNextModel Simulation

Last updated 3 years ago

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You can download the XML specifications for this model here:

Similar to the single SAC example, model Initialization is done using:

# Parse model specifications from the meta-parameters XML file
simulation_parameters = SimulationParameters(
    "simulation_parameters/plexus_SAC_meta.xml",
    note = 'plexus_SAC') 

# Use the model specification to initiate a new simulation
simulation = Simulation(simulation_parameters)

Plot the modeled network morphology:

simulation.plot_morphologies()

Get the soma plot:

simulation.plot_morphologies(soma_plt = True)

The synapse distribution:

Note that BC-SAC synapses are colored in red and SAC-SAC are colored in yellow-green, indicating pre-post synaptic connections.

Similar to a single SAC, you can plot the channel distribution. RSME will generate a plot for each SAC.

5KB
plexus_SAC.zip
archive