MicroFace maps microglial morphology remodeling, revealing spatial zones and bifurcated trajectories during brain microinjury recovery.

Microglia undergo morphological remodeling in response to brain injury, yet large-scale quantification of these changes remains limited. Here, we present MicroFace, an automated image analysis pipeline for high-throughput reconstruction and morphometric profiling of microglia from immunofluorescence images. We applied MicroFace to 279,510 microglia from the rodent cortex following localized microinjury induced by neural probe implantation. Spatiotemporal analysis revealed distinct morphotypes spanning ramified and amoeboid states, organized along spatial gradients relative to the injury site and evolving over time. We identify a bifurcated response characterized by divergent intermediate morphologies, including reactive transient cells and elongated rod-like microglia enriched near the injury. Integration with transcriptomic datasets suggests that rod-like microglia represent a morphologically and transcriptionally distinct subset associated with immunomodulatory functions. These findings define dynamic and heterogeneous microglial adaptations to brain injury and highlight morphology as a key indicator of functional state.