Unveiling Multidimensional Physicochemical Design Principles for Tissue Processing Hydrogels

Abstract A thorough understanding of living systems necessitates detailed mapping of the high‐dimensional molecular landscapes within intact, thick biological tissues. Recent advances in hydrogel‐based tissue processing and clearing techniques have facilitated 3D visualization of biological systems while preserving their native spatial context. Although various polymer hydrogels have been developed for tissue processing, systematic elucidation of their workflow‐dependent properties from a materials science perspective remains lacking, hindering the establishment of design principles for multifunctional performance. Here, a physicochemical design framework for polymer hydrogels in tissue processing is presented, derived from a comprehensive analysis of materials employed in four representative platforms. This analysis encompasses chemo‐rheological parameters, swelling behavior, micro/nanopore morphology, diffusion kinetics, mechanical performance, and thermochemical stability, all of which influence the functional and structural outcomes of the platform. Furthermore, mock tissue‐hydrogel hybrids are engineered using chemically‐fixed protein chunks to evaluate changes in mechanical, morphological, and thermochemical properties in a context relevant to their application. By linking hydrogel design parameters to physicochemical properties and downstream performance in tissue processing, labeling, and imaging, this study establishes a structure‐function blueprint that directly informs rational polymer engineering for high‐throughput, multiscale, and multiplexed molecular tissue imaging applications and beyond.