UC San Diego

Adolescence is an essential period in neurodevelopment in which structural and functional remodeling produces mature cognitive function. These transformations rely on neuroplasticity, the brain’s capacity to adapt at cellular and circuit levels in response to biological changes to maintain functional stability. Several regulators of plasticity have been identified as being highly expressed in the adolescent striatum. The glycoprotein Reelin, encoded by the Reln gene, and cannabinoid receptor 1, encoded by Cnr1, are associated with neuronal maturation, synaptic plasticity and regulation, and reward processing. However, the spatial relationship between Cnr1 and Reln within developing striatal tissue is still poorly characterized. Quantifying this organization may reveal how coordinated regulation of Reelin and cannabinoid pathways play a role in shaping adolescent striatal plasticity. This thesis describes the development and application of a customized pipeline in Cell Profiler, an open-source image analysis platform that enables automated, modular image processing and quantitative measurement, and Python, visualizing the calculated metrics in normalized spatial heatmaps. The analysis was applied to images of Reln and Cnr1 signaling in the adolescent mouse striatum derived from multiplex RNA fluorescence in situ hybridization (RNA-FISH). Cell-level intensity quantification was further evaluated for directional gradients and regional heterogeneity with correlation metrics and Kullback–Leibler divergence. When applied to multiple samples, signal intensities corresponding to Cnr1 and Reln were observed to form overlapping, correlated gradients with increased enrichment in the dorsolateral striatum. This work demonstrates a methodology for quantifying and visualizing gradients of single-cell signaling intensity in tissue from the adolescent mouse striatum.