Intravital Microscopy to Continuum In Silico Simulation of Flow-mediated Transport in Blood Clot Neighborhoods

Pathological blood clotting, or thrombosis, is the primary underlying cause of stroke and heart attack. Complications occur by a clot obstructing flow or embolization causing occlusion downstream. Understanding flow and flow-mediated transport in blood clot neighborhoods under physiologically realistic conditions is essential to discerning disease etiology. In silico techniques have emerged as a powerful approach to studying flow conditions in and around blood clots. Existing in silico methods, however, are often limited to idealized or static clot geometries. Here, we circumvent this limitation by bridging the gap between in silico techniques and in vivo imaging. Intravital microscopy provides a time-ordered series of high-resolution images characterizing the process of clot development in living animals. Leveraging intravital microscopy data we present an image segmentation methodology to obtain a data-driven dynamic clot configuration from mouse cremaster injury experiments. We illustrate unsteady flow and flow-mediated transport in the segmented clot neighborhood during clot development and identify coherent structures which organize advective transport around a dynamic blood clot.