StarTrack Morphometric Profiling of Glial Clones in Adult Brain Damage Models

This chapter provides a step-by-step protocol for applying StarTrack-based lineage tracing to characterize glial clones, derived from embryonic neural stem cells in the adult mouse brain following injury. We detail in vivo delivery of multicolor StarTrack plasmids via in utero electroporation, and induction of Traumatic Brain Injury (TBI), and Experimental Autoimmune Encephalomyelitis (EAE) in adult animals. High-resolution confocal Z-stack imaging is combined with Fiji/ImageJ-based workflows, including the Simple Neurite Tracer plugin, to segment individual clones and reconstruct three-dimensional cell architectures. Standardized morphometric parameters, soma volume, process length, branching complexity, Sholl analysis, and spatial dispersion, are extracted and normalized. Finally, multivariate statistical approaches are outlined to compare clonal adaptations across injury models. This integrated methodology enables robust, reproducible assessment of glial proliferation, migration, and morphological plasticity in central nervous system lesions, offering novel insights into their roles in repair, inflammation, and demyelination.