A modular tissue-clearing framework integrated with light-field microscopy enables rapid volumetric phenotyping of cardiac tissue

Tissue clearing has transformed volumetric imaging by improving optical access to thick tissues, yet most existing protocols remain rigid and fail to accommodate the biochemical diversity of different samples. Here, we introduce a question-oriented modular framework that enables flexible assembly of clearing and imaging pipelines tailored to specific biological objectives. By systematically optimizing each module to preserve endogenous fluorescence, antigenicity, and tissue integrity while achieving high transparency and protein retention, we demonstrate its use across diverse cardiac applications—development, infarction and regeneration, as well as immune and vascular mapping—showing that different questions require distinct module assemblies and parameters. Coupled with light-field microscopy (LFM), the workflow efficiently captures submillimeter sections with 30–100-fold smaller datasets and rapid computational reconstruction, enabling high-throughput quantitative volumetric analysis. Together, this modular framework and imaging integration provide a rational and practical foundation for adaptable and interoperable 3D analyses of regenerative, pathological, and comparative systems across vertebrate models.