Visualization and quantification of the stromal-vascular compartment in fetal or adult mouse bones: From sampling to high-resolution 3D image analysis

Advanced techniques combining tissue clearing, deep confocal imaging, and image quantification enable researchers to characterize complex tissue architectures and understand how trauma or disease impact on their respective components. Here, we detail methodologies to prepare, immunostain, and clear thick sections of mouse bones. We describe their use to visualize and quantitatively analyze marrow blood vessels and their spatial relationship with stromal skeletal stem/progenitor cells. These approaches can help unravel the stromal-vascular interplay in the bone marrow environment in health and disease. For complete details on the use and execution of this protocol, please refer to Mesnieres et al. (2021).