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Abstract
The thalamus, a major subcortical structure, relays sensory and motor signals to the cortex and striatum. This study introduces a method for mapping thalamic projections to delineate nuclei based on connectivity patterns. Multi-color fluorescent proteins were stereotaxically injected into small thalamic cell subsets, and labeled brains were serially sectioned, imaged, and reconstructed into normalized 3D volumes using Matlab. Regions of interest in cortex and striatum were manually segmented, and injections were scored by anatomical connectivity. This mesoscopic connectome approach enables comprehensive visualization of long-range thalamic projections, providing a framework for structural parcellation and investigation of complex neural circuits.