Highlights d Auditory gamma entrainment using sensory stimuli (GENUS) boosts hippocampal function d GENUS affects microglia, astrocytes, and vasculature in auditory cortex and hippocampus d Auditory plus visual GENUS induces microglia clustering around plaques d Auditory plus visual GENUS reduces amyloid pathology throughout neocortex

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Author contributions T.K. and K.C. designed the experiments and wrote the paper with input from other authors. T.K. developed ELAST and conducted hydrogel experiments, evaluation of mechanical properties and tissue deformation, antibody screening and delivery tests, and the deeptissue labeling experiment. W.G. modeled the diffusion profiles in hydrogels and conducted the cyclic compression experiment to assess depth-wise immunostaining quality. N.B.E., T.K. and W.G. developed and operated the cyclic compression device. N.B.E. formulated the RI-matching media. C.H.S. and T.K. established the mouse SHIELD protocol for ELAST. C.H.S. conducted the in situ hybridization experiment. A.A. and W.G. conducted the organoid experiment. J.-G.K. and T.K. conducted the downstream histology experiment. M.P.F. provided the human brain tissue specimens. K.C. supervised all aspects of the work. Competing interestsThe ELAST concepts and applications are covered in a pending patent application owned by MIT (K.C. and T.K.). K.C. is a cofounder of LifeCanvas Technologies, a startup that provides solutions for 3D tissue processing. Data availabilityAll data supporting the findings of this study are included in figures and videos as representative images or data points in the plots.

Studying the function and dysfunction of complex biological systems necessitates comprehensive understanding of individual cells. Advancements in three-dimensional (3D) tissue processing and imaging modalities have enabled rapid visualization and phenotyping of cells in their spatial context. However, system-wide interrogation of individual cells within large intact tissue remains challenging, low throughput, and error-prone owing to the lack of robust labeling technologies.Here we introduce a rapid, versatile, and scalable method, eFLASH, that enables complete and uniform labeling of organ-scale tissue within one day. eFLASH dynamically modulates chemical transport and reaction kinetics to establish system-wide uniform labeling conditions throughout the day-long labeling period. This unique approach enables the same protocol to be compatible with a wide range of tissue types and probes, enabling combinatorial molecular phenotyping across different organs and species. We applied eFLASH to generate quantitative maps of various cell types in mouse brains. We also demonstrated multidimensional cell profiling in a marmoset brain block. We envision that eFLASH will spur holistic phenotyping of emerging animal models and disease models to help assess their functions and dysfunctions.

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