Multiscale symbolic morpho-barcoding reveals region-specific and scale-dependent neuronal organization

Neuronal morphology shapes circuit organization, yet its multiscale complexity has hindered systematic brain-wide analysis. Here, we introduce multiscale morpho-barcoding (MMB), a framework that encodes whole-brain neuronal morphology into symbolic barcodes spanning cellular geometry, axonal tract routing, arbor organization, and predicted presynaptic distributions. Applying MMB to 1,876 fully reconstructed mouse neurons, comprising 3,776 arbors, and 2.63 million predicted presynaptic sites, we identified distinct multiscale morpho-patterns that help reveal two organizational principles. First, neuronal morphology is region specific: regional identity arises from distinct combinations of shared and region-biased morpho-motifs. Second, organization is scale dependent: different morphological scales contribute differentially to the neuronal classification and circuit architecture. Within this mouse dataset, MMB discriminates major anatomical divisions and resolves canonical thalamic circuit classes, exceeding the resolution of projection strength-based representations. MMB provides an interpretable and scalable framework for integrating morphology with connectivity and function. This framework could further be applicable to analyze disease-oriented structural phenotypes.