pynn_brainscales.brainscales2.examples.manual_morphology_builder

In this example, we show how neuron circuits on BrainScales-2 can be connected to form multi-compartmental neuron models.

We explicitly define the location of the different neuron circuits and how they are connected. This gives us full control over the configuration of the circuits but can be tedious for larger models.

In the example ‘morphology_builder.py’ we show how you can define an abstract graph of your multi-compartmental neuron model and use the automatic mapping algorithm to map it to BrainScaleS-2.

Classes

PlacedCompartment(*, positions, label, …)

A single iso-potential compartment of a multi-compartmental neuron model.

SharedLineConnection(start, stop, row)

Functions

pynn_brainscales.brainscales2.examples.manual_morphology_builder.create_mc_neuron(name: str, compartments: List[pynn_brainscales.brainscales2.morphology.parts.PlacedCompartment], connections: Optional[List[pynn_brainscales.brainscales2.morphology.parts.SharedLineConnection], None] = None, single_active_circuit: bool = False) → pynn_brainscales.brainscales2.morphology.mc_neuron_base.McNeuronManualBase

Create a multi-compartment neuron class from manually placed compartments.

This methods uses manually placed compartments, checks that the configuration is valid and generates a neuron class. Furthermore, the connection between the different neuron circuits has to be defined manually.

Parameters

  • name – Name of the newly created class.

  • compartments – Compartments of the multi-compartment neuron.

  • connections – Specifies where the shared line is connected.

  • single_active_circuit – Disable leak, capacitance and threshold for all but the first circuit in each compartment.

Returns

Class for a multi-compartmental neuron model with the given compartments and connections.

pynn_brainscales.brainscales2.examples.manual_morphology_builder.create_neuron_class(length: int)

Create a neuron class for a dendritic chain.

Parameters

length – Number of compartments in the chain.

pynn_brainscales.brainscales2.examples.manual_morphology_builder.main(length: int = 3, runtime: float = 0.15)

Create a chain of compartments.

Record the membrane voltage in each compartment while inputs are injected in the different compartments.

Parameters

  • length – Length of the chain.

  • runtime – Experiment runtime in ms. Note that for runtimes over around 0.15 ms, samples from the CADC are lost, i.e. the data is not recorded of the whole experiment time.