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Using the manual AIR System from Cell Microsystems (no longer sold) nuclei was manually selected under a microscope for isolation. The nuclei were stained and extracted from the Array via manual isolation using the first-generation system attached to the microscope. Neuronal nuclei were distinguished from others visually, examining the diameter, chromatin condensation, and locating oligodendroglia using olig2. CellRaft allowed for visual review that reduced the chance of droplets compared to fluorescence-activated nuclear sorting (FANS). Photographs before isolation allowed the direct correlation with individual cell WGS results. The neuronal nuclei extracted in this paper were used to study Parkinson’s disease and multiple system atrophy through identifying the copy number variants in synucleinopathies.