Biologically Detailed Brain Cell Modeling in BrainX

braincell provides a unified interface for biophysically detailed brain cell models — from single-compartment Hodgkin-Huxley neurons to fully morphological multi-compartment cells with realistic dendrites and axons. It is built on top of JAX and brainstate, offering highly parallelized, differentiable simulation of biologically realistic neural dynamics.

Features

• Single-compartment neurons — braincell.SingleCompartment with a rich library of ion channels (Na, K, Ca, HCN, K-Ca) and numerical integrators.
• Multi-compartment cells — braincell.Cell with declarative mechanism painting (cell.paint) and point-process placement (cell.place) onto morphological regions.
• Morphology system — braincell.morph: immutable Branch geometry, typed subclasses (Soma, Dendrite, Axon, BasalDendrite, ApicalDendrite), and the mutable Morphology tree.
• IO readers — SWC, ASC, and NeuroML2 file readers; a full NeuroMorpho.Org client with search, download, and local caching.
• Visualization — braincell.vis: 2D tree layouts (matplotlib) and 3D rendering (PyVista / Plotly), color-by-values, morphometry plots, and movie export.
• Integrator registry — braincell.quad: explicit (Euler, RK2/3/4), implicit, exponential-Euler, and staggered cable solve, all selectable by name.
• Declarative mechanisms — braincell.mech: Channel, Ion, CableProperty, CurrentClamp, Synapse, Junction specs for the Cell frontend.
• CLI — braincell-neuromorpho command for searching and downloading from NeuroMorpho.Org.

Quick start

Single-compartment neuron

importbraincellimportbrainstateimportbraintoolsimportbrainunitasuclassHTC(braincell.SingleCompartment):
def__init__(self, size, solver: str='ind_exp_euler'):
super().__init__(size, V_initializer=braintools.init.Constant(-65.*u.mV), V_th=20.*u.mV, solver=solver)
self.na=braincell.ion.SodiumFixed(size, E=50.*u.mV)
self.na.add(INa=braincell.channel.Na_Ba2002(size, V_sh=-30*u.mV))
self.k=braincell.ion.PotassiumFixed(size, E=-90.*u.mV)
self.k.add(IKL=braincell.channel.K_Leak(size, g_max=0.01* (u.mS/u.cm**2)))
self.k.add(IDR=braincell.channel.KDR_Ba2002(size, V_sh=-30.*u.mV, q10=2.0, temp=u.celsius2kelvin(16.)))
self.ca=braincell.ion.CalciumDetailed(size, C_rest=5e-5*u.mM, tau=10.*u.ms, d=0.5*u.um)
self.ca.add(ICaL=braincell.channel.CaL_IS2008(size, g_max=0.5* (u.mS/u.cm**2)))
self.ca.add(ICaT=braincell.channel.CaT_HM1992(size, g_max=2.1* (u.mS/u.cm**2)))
self.kca=braincell.MixIons(self.k, self.ca)
self.kca.add(IAHP=braincell.channel.AHP_De1994(size, g_max=0.3* (u.mS/u.cm**2)))
self.Ih=braincell.channel.HCN_HM1992(size, g_max=0.01* (u.mS/u.cm**2), E=-43*u.mV)
self.IL=braincell.channel.IL(size, g_max=0.0075* (u.mS/u.cm**2), E=-70*u.mV)

Multi-compartment cell

Build a morphological neuron from an SWC file and paint ion channels onto it declaratively:

importbraincellimportbraincell.mechasmechimportbrainunitasufrombraincell.filterimportAllRegion, RootLocation, branch_in# Load morphology from SWCmorpho=braincell.Morphology.from_swc("path/to/neuron.swc")
# Declare and simulate a multi-compartment cellcell=braincell.Cell(morpho)
# Paint passive cable properties everywherecell.paint(AllRegion(), mech.CableProperty(
resting_potential=-65.0*u.mV,
membrane_capacitance=1.0*u.uF/u.cm**2,
axial_resistivity=100.0*u.ohm*u.cm,
))
# Paint ion channels onto specific regionscell.paint(AllRegion(), mech.Channel("IL", g_max=0.0003*u.S/u.cm**2, E=-70*u.mV))
cell.paint(branch_in("type", "soma"), mech.Channel("INa_Ba2002", g_max=0.12*u.S/u.cm**2))
cell.paint(
branch_in("type", ("dendrite", "basal_dendrite", "apical_dendrite")),
mech.Channel("ICaL_IS2008", g_max=0.002*u.S/u.cm**2),
)
# Inject current at the somacell.place(RootLocation(0.5), mech.CurrentClamp(delay=10*u.ms, durations=50*u.ms, amplitudes=0.2*u.nA))

Morphology and visualization

importbraincellimportbraincell.visasvis# Load from NeuroMorpho.Org by neuron id (downloaded and cached locally)morpho=braincell.Morphology.from_neuromorpho(12345)
# 2-D layout plotvis.plot2d(morpho)
# 3-D renderingvis.plot3d(morpho)

Installation

pip install braincell --upgrade

Optional dependency groups:

Extra	What it installs
braincell[vis]	matplotlib, pyvista, plotly (visualization backends)
braincell[io]	requests (NeuroMorpho.Org client)
braincell[all]	all of the above
braincell[cpu]	jax[cpu]
braincell[cuda12]	jax[cuda12]

For example, to install with visualization and IO support:

pip install "braincell[vis,io]" --upgrade

Alternatively, install BrainX to get braincell together with the rest of the brain modeling ecosystem:

pip install BrainX -U

Documentation

The official documentation is hosted on Read the Docs: https://brainx.chaobrain.com/braincell

See also the ecosystem

BrainCell is one part of our brain modeling ecosystem: https://brainx.chaobrain.com/