In conventional pathology and physiology research, two-dimensional (2D) analysis—observing thinly sliced tissue sections—has been mainstream, making it difficult to comprehensively understand the distribution of cells across entire organs or throughout the whole organism. Therefore, a new analytical platform has been needed to quantitatively elucidate developmental processes of the organism, drug efficacy and adverse effects, and disease-related changes at the whole-organ or whole-body level.