braincell module

Base Class for Cell Modeling

HHTypedNeuron	The base class for the Hodgkin-Huxley typed neuronal membrane dynamics.
SingleCompartment	Base class to model conductance-based neurons with single compartment.
Cell	Multi-compartment cell with explicit declaration / initialization phases.
RunResult	Return value of Cell.run().

Base Class for Ion Channels

IonChannel	Base class for modeling ion channel dynamics in neuronal simulations.
Ion	The base class for modeling ion dynamics in neuronal simulations.
IonInfo	A named tuple representing the information of an ion in a neuron model.
MixIons	A class for mixing multiple ion channels in neuronal simulations.
Channel	The base class for modeling channel dynamics in neuronal simulations.

Ion Helpers

mix_ions

Create a mixed ion channel by combining multiple ion instances.

Discretization: Control Volumes and Policies

Static, declaration-time representation of how a multi-compartment cell is divided into control volumes (CVs), plus the policies that decide how many CVs each branch receives.

CV	Immutable per-control-volume record exposed to users.
CVTree	Graph-level metadata for one CV discretization.
Node	Point-space thin view of one or more CV-local positions.
NodeTree	Point-space view of a cell's declaration-time discretization.
CVPolicy	Base class for morphology-to-CV discretization policies.
CVPerBranch	Assign the same number of CVs to every branch.
CVPolicyByTypeRule	One branch-type dispatch rule for CompositeByTypePolicy.
CompositeByTypePolicy	Dispatch different CV policies by morphology branch type.
DLambda	Splits each branch using the NEURON-style d_lambda discretization.
MaxCVLen	Split branches so each CV stays below a target physical length.

Morphology

Neuronal morphology container and the branch types used to label sections of a reconstruction.

Morphology	Mutable morphology tree for authoring, querying, and visualization.
Branch	Immutable geometry primitive representing an anatomical branch.
Soma	A Branch with type fixed to "soma".
Dendrite	A Branch with type fixed to "dendrite".
Axon	A Branch with type fixed to "axon".
BasalDendrite	A Branch with type fixed to "basal_dendrite".
ApicalDendrite	A Branch with type fixed to "apical_dendrite".
CustomBranch	A Branch with type fixed to "custom".

Stimulus and Cable Mechanisms

Passive cable properties and stimulus clamps attachable to a cell. See braincell.mech module for the full declarative mechanism layer.

CableProperty	Passive cable properties of a region.
CurrentClamp	Piecewise-constant current clamp.
SineClamp	Sinusoidal current clamp.
FunctionClamp	Arbitrary-callable current clamp.