MarrowQuant, a digital and quantitative pathology tool was used to quantify the different compartments within the bone marrow at different conditions, mainly aplasia and aging conditions. By using our tool, we can compare the skeletal map induced by lethal irradiation(aplasia), with longitudinal quantification of the “red-to-yellow-to-red” transition over 2 months (aging) in C57BL/6 mouse femurs and tibiae.