NeuWalk: A Python Library for Data-Driven Synthesis of Neuron Morphologies Using Random Walks

Abstract

Large-scale biophysically-detailed models of the brain are instrumental in unraveling how cellular, synaptic, and circuit-level mechanisms contribute to neural dynamics. Such models are built around large populations of single-neuron models whose morphologies must preserve physiological variability to reproduce integrative properties and firing patterns observed experimentally. Experimental reconstruction of morphologies is a time-consuming and resource-intensive process, unlikely to supply them at the required scale. Several data-driven methods for morphology synthesis have been developed, which nonetheless rely on extensive datasets for parameter estimation. To address this limitation, we developed NeuWalk, to our knowledge the first public Python library for morphology synthesis based on branching-and-annihilating, biased-and-correlated random walks. It estimates branching and annihilation rates from Sholl intersections and, optionally, bifurcation counts, while also ensuring their replication in synthetic morphologies; user-specified combinations of biases, implementing somatofugality, self-avoidance, spatial competition, and branching-angle control, sculpt morphological patterns characteristic of each neuron class. We then validated the method on mitral and middle tufted cells of the olfactory bulb, semilunar and pyramidal cells of the anterior piriform cortex, and neocortical pyramidal neurons: means and variances of Sholl intersections, bifurcation counts, and total dendritic length were statistically indistinguishable between synthetic and natural morphologies, with the single exception of its variance in apical dendrites of piriform cortex pyramidal neurons. As Sholl intersections and bifurcation counts are commonly reported in the literature, and biases can be inferred from published images or qualitative descriptions, NeuWalk requires no immediate access to experimental reconstructions, striking a trade-off between data-driven parameterization and empiricism without sacrificing morphological accuracy.