Preparation of cleared whole-mount urethra and urinary bladder from transcardially perfused mice for immunolabeling and analysis by CLSM.

The distribution of cells within organs, their involvement in tissue structure, and their organization in three-dimensional networks are important aspects in the analysis and understanding of biological processes. Here, we present a protocol for preparing whole-mount urethra and urinary bladder from transcardially perfused mice for immunolabeling and analysis by confocal laser scanning microscopy. We describe steps for perfusion, preparation, tissue clearing, and analysis using confocal laser scanning microscopy. We then detail procedures for three-dimensional processing of the murine urethra and urinary bladder. For complete details on the use and execution of this protocol, please refer to Schmidt et al.1.