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Parkinson's disease (PD) is a neurodegenerative disorder characterized with the progressive loss of dopaminergic (DA) neurons within the substantia nigra pars compacta (SNc). Quantitative analysis of neuronal loss including neuronal processes, axons and dendrites, would advance the understanding of the pathogenesis of PD. ScaleS, an aqueous tissue clearing method, provides stable tissue preservation while maintaining potent clearing capability, allowing quantitative three-dimensional (3D) imaging of biological tissues. In this chapter,