Morphometric analysis of the thymic epithelial cell network using integrated and orthogonal digital pathology approaches

The thymus, a central organ for T cell development, lacks standardized pathology methods to assess its structure and function. Most studies rely on flow cytometry, which profiles thymic cell populations but offers limited spatial insight into tissue organization. This gap restricts our understanding of how physiological or pathological conditions remodel thymic architecture and impact immune competence. Here, we introduce a digital pathology pipeline that integrates analytical algorithms with rationalized morphometric assessments at tissue-wide, microanatomical, and ultrastructural levels. We develop and validate it using a mouse model of age-dependent thymic involution, characterized by cortical atrophy, medullary expansion, and epithelial disorganization, providing a benchmark for quantifying known lesions and testing reproducibility. As a proof-of-concept, we apply the pipeline to a DMBA-induced carcinogenesis model combined with early-life cholera toxin (CT) exposure, to evaluate whether environmental stimulation (“hygiene hypothesis”) mitigates late-stage thymic pathology. CT normalizes select parameters, particularly in the medulla, including reduced perivascular space and mTEC density, suggesting enhanced thymocyte occupancy. Overall, this versatile and scalable pipeline provides a standardized framework for quantitative evaluation of thymic structure, supporting both basic and translational studies of thymic biology and disease. A new digital pathology pipeline enables multiscale, quantitative analysis of thymic structure, revealing age-dependent epithelial remodeling and showing improved medullary regeneration after early-life immune modulation in a carcinogenesis model.