Real-time single-particle imaging of functional lungs reveals mosaic-like patterns of aerosol deposition in alveoli

Inhaled pathogens, pollutants and therapeutics interact with the dynamic architecture of the alveoli, yet how individual particles move and deposit at cellular resolution remains unclear. Here, utilizing the crystal ribcage platform, we track aerosol transport in ex vivo, actively ventilated lungs using real-time fluorescence imaging with single-particle resolution, capturing droplet trajectories, free-flight motion, impact orientation and deposition timescales within functional alveoli. These measurements show that intra-alveolar transport is directional and shaped by airway-guided flow and tissue motion. At larger scales, aerosols do not disperse uniformly throughout the lung's volume but instead concentrate into geometrically constrained clusters of alveoli, forming a conserved mosaic-like compartmentalization while neighbouring alveoli remain largely unexposed. The pattern persists across particle types and species and varies with particle properties and lung age. In models of emphysema, fibrosis and metastasis, airway remodelling alters both the geometry and amount of deposition. These multiscale insights reveal how single-particle transport and airway structure together shape alveolar exposure, immune activation, development and therapeutic accessibility.