Neonatal brain injury, caused by hypoxia-ischemia, is a major cause of neurological disability. Therapeutic hypothermia (TH) is the current standard of care for a subgroup of babies born with brain injury, but 50% of babies treated with TH still have poor outcomes. Initiated by hypoxia-ischemia, inflammatory processes contribute both to cell damage and tissue remodeling. During development, changes in the brain extracellular matrix (ECM) structure and composition have been shown to affect cell migration, proliferation, synaptic plasticity, and tissue architecture. However, the relationship between neuroinflammation and ECM reorganization remains largely unexplored in the neonatal brain. There is a need to characterize the brain microenvironment following neonatal brain injury to better understand disease progression. Nanoparticles, which have proven capable of probing biological systems, can be an optimal platform for evaluating structural changes in brain ECM as a function of normal or pathological processes. We aim to characterize ECM structural changes in multiple brain regions in an oxygen glucose deprivation (OGD) brain slice model in rats that has neuropathological hallmarks of hypoxic-ischemic (HI) brain injury. For this, 300 μm-thick organotypic whole hemisphere brain slices were prepared from postnatal day 28 rats. Slices were incubated for 2 hours in an oxygen-deprived chamber with media lacking glucose and pathological changes are observed after 24 hours. We perform multiple particle tracking (MPT) to quantify nanoparticle diffusion in ECM, immunohistochemistry to visualize the ECM and inflammatory processes such as mitochondrial morphology, and RT-qPCR to obtain ECM mRNA expression data. This combinatorial approach will capture changes in ECM structure at different time and length profiles. We have found mitochondrial fission and upregulation of inflammatory cytokines, demonstrating our ability to induce neuroinflammation in slices. By combining nanoscale diffusion data with micron-scale structural data, our findings will provide new insights into pathology-dependent ECM structural changes in neonatal brain injury.