API reference

Modules

jaxley.Compartment	A single compartment.
jaxley.Branch	A branch made up of one or multiple compartments (without branchpoints).
jaxley.Cell	A cell made up of one or multiple branches (with branchpoints).
jaxley.Network	A network made up of multiple cells, connected by synapses.

Simulation

jaxley.integrate	Solves ODE and simulates neuron model.
jaxley.integrate.build_init_and_step_fn	Return init_fn and step_fn which initialize modules and run update steps.

Morphologies

jaxley.read_swc	Reads SWC file into a Cell.
jaxley.morphology.distance_direct	Returns the direct distance between a root and other compartments.
jaxley.morphology.distance_pathwise	Returns the pathwise distance between a root and other compartments.
jaxley.morphology.morph_delete	Deletes part of a morphology.
jaxley.morphology.morph_connect	Combines two morphologies into a single cell.

Channels

jaxley.channels.Channel	Channel base class.
jaxley.channels.HH	Hodgkin-Huxley channel based on Sterratt, Graham, Gillies & Einevoll.
jaxley.channels.Izhikevich	Izhikevich neuron model.
jaxley.channels.Rate	Rate-based, unit-less, neuron model.
jaxley.channels.Fire	Mechanism to reset the voltage when it crosses a threshold.
jaxley.channels.Na	Sodium channel based on Pospischil et al., 2008.
jaxley.channels.K	Potassium channel based on Pospischil et al., 2008.
jaxley.channels.Leak	Leak current based on Pospischil et al., 2008.
jaxley.channels.Km	Slow M Potassium channel based on Pospischil et al., 2008.
jaxley.channels.CaL	L-type Calcium channel based on Pospischil et al., 2008.
jaxley.channels.CaT	T-type Calcium channel based on Pospischil et al., 2008.

Pumps

jaxley.pumps.Pump	Pump base class.
jaxley.pumps.CaFaradayConcentrationChange	Update the intracellular calcium ion concentration depending on calcium current.
jaxley.pumps.CaNernstReversal	Compute Calcium reversal from inner and outer concentration of calcium.
jaxley.pumps.CaPump	Calcium dynamics based on Destexhe et al. 1994.

Synapses

jaxley.synapses.Synapse	Base class for a synapse.
jaxley.synapses.IonotropicSynapse	Compute synaptic current and update synapse state for a generic ionotropic synapse.
jaxley.synapses.TanhRateSynapse	Compute synaptic current for tanh synapse (no state).
jaxley.synapses.TanhConductanceSynapse	Compute synaptic current for a simple conductance synapse (no state).

Connectivity

jaxley.connect.connect	Connect specific compartments of a network with a synapse.
jaxley.connect.connectivity_matrix_connect	Connect cells of a network with synapses via a boolean connectivity matrix.
jaxley.connect.fully_connect	Fully (densely) connect cells of a network with synapses.
jaxley.connect.sparse_connect	Sparsely connect cells of a network with synapses.

Optimization

jaxley.optimize.transforms.SigmoidTransform	Sigmoid transformation.
jaxley.optimize.transforms.SoftplusTransform	Softplus transformation.
jaxley.optimize.transforms.NegSoftplusTransform	Negative softplus transformation.
jaxley.optimize.transforms.AffineTransform
jaxley.optimize.transforms.ChainTransform	Chaining together multiple transformations
jaxley.optimize.transforms.MaskedTransform
jaxley.optimize.transforms.CustomTransform	Custom transformation.
jaxley.optimize.optimizer.TypeOptimizer	optax wrapper which allows different argument values for different params.

Graph backend

jaxley.io.graph.to_swc_graph	Read a SWC file and return a SWC graph via networkX.
jaxley.io.graph.build_compartment_graph	Return a networkX graph that indicates the compartment structure.
jaxley.io.graph.vis_compartment_graph	Visualize a compartment graph.
jaxley.io.graph.from_graph	Return a Jaxley module from a compartmentalized networkX graph.
jaxley.modules.base.to_graph	Export a jx.Module as a networkX compartment graph.