Biologically Detailed Brain Cell Modeling

braincell provides a unified interface for modeling single-compartment and multi-compartment Hodgkin-Huxley-styled neuron models. It is built on top of JAX and brainstate, offering a highly parallelized and efficient simulation of biophysically detailed brain cell models.

Features

• Biophysical State Precision: BrainCell enables biophysically accurate modeling of neural dynamics across scales, from ion channel gating to network-wide population activity.

• Stiff Dynamics Optimization: Features specialized solvers optimized for stiff neural systems, efficiently handling rapid biophysical transitions.

• JAX-based: Leverages JAX for high-performance computing, automatic differentiation, and compilation to XLA (CPU/GPU/TPU).

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Installation

CPU

pip install -U braincell[cpu]

GPU (CUDA)

pip install -U braincell[cuda12]

# or
pip install -U braincell[cuda13]

TPU

pip install -U braincell[tpu]

Quick Start

Here is an example to model a single-compartment thalamus neuron model:

import braincell
import brainstate
import braintools
import brainunit as u

class HTC(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.INa_Ba2002(size, V_sh=-30 * u.mV))

        self.k = braincell.ion.PotassiumFixed(size, E=-90. * u.mV)
        self.k.add(IKL=braincell.channel.IK_Leak(size, g_max=0.01 * (u.mS / u.cm ** 2)))
        self.k.add(IDR=braincell.channel.IKDR_Ba2002(size, V_sh=-30. * u.mV, phi=0.25))

        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.ICaL_IS2008(size, g_max=0.5 * (u.mS / u.cm ** 2)))
        self.ca.add(ICaN=braincell.channel.ICaN_IS2008(size, g_max=0.5 * (u.mS / u.cm ** 2)))
        self.ca.add(ICaT=braincell.channel.ICaT_HM1992(size, g_max=2.1 * (u.mS / u.cm ** 2)))
        self.ca.add(ICaHT=braincell.channel.ICaHT_HM1992(size, g_max=3.0 * (u.mS / u.cm ** 2)))

        self.kca = braincell.MixIons(self.k, self.ca)
        self.kca.add(IAHP=braincell.channel.IAHP_De1994(size, g_max=0.3 * (u.mS / u.cm ** 2)))

        self.Ih = braincell.channel.Ih_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)

Ecosystem

BrainCell is one part of our brain modeling ecosystem.