In Vivo Network-Level Cerebrovascular Mapping Reveals the Impact of Flow Topology on Capillary Stalls After Stroke

Cerebral microvasculature is essential for brain function, but how flow and large-scale connectivity contribute to its resilience or failure remains poorly understood. To address this, we developed OMNIMap, a framework that integrates extended-focus optical coherence microscopy, learning-based segmentation and vessel-graph optimization, linking capillary flow and stalls to broader network context. Imaging over 60,000 capillaries in the mouse cortex revealed heterogeneous vascular responses to stroke, with capillary stalls, flow increases and decreases within the same networks. Divergent-to-convergent capillary subtypes had the highest stall risk. This association was not fully explained by differences in vessel structure, velocity or network position, suggesting that additional factors contribute to their vulnerability. Despite changes in individual capillary assignments after stroke, the overall proportions of capillary subtype remained largely preserved. Longitudinal mapping further showed that capillary stalls may persist until at least 7 days post-stroke. Together, these findings identify local flow topology as a marker of capillary vulnerability after stroke.