Cutting-edge single-cell RNA sequencing and multiplexed imaging advances deepen insights into complex diseases, including breast cancer heterogeneity and autoimmune disorders. Novel quantitative frameworks integrate genomic, transcriptomic, and proteomic data to characterize tumor cell diversity and immune responses at unprecedented resolution. Additionally, the TACIT AI algorithm accelerates cellular type identification in complex tissues, enhancing biomarker discovery for immunotherapy. These innovations pave the way for personalized treatment strategies targeting molecular and cellular disease landscapes.