SynClear: A one-step synchronous clearing and labeling strategy for multiscale 3D brain mapping

High-resolution three-dimensional imaging is essential for resolving the multiscale organization of biological tissues. However, conventional workflows treat tissue clearing and molecular labeling as separate steps, leading to a kinetic mismatch between reagent transport and probe binding that limits imaging depth, labeling uniformity, and throughput. Here, we introduce SynClear, a one-step strategy that synchronizes nuclear labeling with tissue clearing by embedding fluorescent probes within a chemically engineered clearing medium. This integrated formulation enables rapid and uniform labeling across millimeter-scale samples while preserving endogenous fluorescence and remaining compatible with multiplexed immunostaining. We demonstrate the general applicability of SynClear across diverse tissue types, including mouse brain, peripheral organs, and post-mortem human cortex. In mouse brain sections, SynClear supports accurate 3D atlas registration and quantitative mapping of cytoarchitecture. In glioblastoma models, it resolves pathological features across scales, from tumor boundaries to immune microenvironments. In human cortex, it enables laminar-resolved structural analysis and neuronal subtype mapping. By coupling labeling and clearing within a single chemical framework, SynClear provides a robust and scalable platform for volumetric tissue imaging, with potential applications in both basic neuroscience and translational pathology.