MDISCO: A High-Throughput Tissue-Clearing Protocol for Preservation of Endogenous Fluorescence in Whole Mouse Brains

Organic solvent-based tissue clearing methods are widely used for whole-brain imaging but often compromise endogenous fluorescence. Existing protocols, such as iDISCO and fluorescence-preserving variants, have improved optical transparency but still present trade-offs between fluorescence retention, tissue stability, and workflow complexity. Here, we present MDISCO, a modified iDISCO-based clearing protocol designed to enhance preservation of endogenous fluorescence while maintaining high transparency and stable tissue morphology. MDISCO is directly compared with FDISCO+, an established fluorescence-preserving protocol, for the preservation of endogenous tdTomato and YFP. Performance across clearing steps is evaluated by measuring brain weight, anteroposterior and mediolateral dimensions, and optical transparency before and after solvent clearing and refractive index matching. Fluorescence preservation is assessed using whole-brain light-sheet microscopy with standardized imaging parameters to enable direct comparison. This protocol provides an accessible and high-throughput, reproducible workflow for solvent-based clearing with robust endogenous fluorescence preservation, offering clear advantages for whole-brain 3D imaging of genetically encoded fluorescent reporters. Key features • Preserves endogenous tdTomato and YFP fluorescence in whole mouse brains without signal amplification through immunolabeling. • Improves optical clarity and cellular resolvability while maintaining anatomical integrity. • Supports high-throughput "clearing" of whole-tissue samples.