Traumatic brain injury (TBI) results in a cascade of cellular responses, which produce neuroinflammation, partly due to microglial activation. Transforming from surveying to primed phenotypes, microglia undergo considerable molecular changes. However, specific microglial profiles in rat remain elusive due to tedious methodology and limited availability of reagents. Here, we present a flow cytometry-based analysis of rat microglia 24 h after TBI using the controlled cortical impact model, validated with a bioinformatics approach. Isolated microglia are analyzed for morphological changes and their expression of activation markers using flow cytometry, traditional gating-based analysis methods and support the data by employing bioinformatics statistical tools. We use CD45, CD11b/c, and p2y12 receptor to identify microglia and evaluate their activation state using CD32, CD86, RT1B, CD200R, and CD163. The results from logic-gated flow cytometry analysis was validated with bioinformatics-based analysis and machine learning algorithms to detect quantitative changes in morphology and marker expression in microglia due to activation following TBI. Traumatic brain injury (TBI) is attributed to a third of all injury-related deaths in the United States 1. Each year, 1.7 million people receive treatment for brain trauma, and more than 5 million people receive treatment for TBI-related complications and disabilities. TBI can occur in a variety of circumstances and a range of severity levels, which lead to cognitive and behavioral changes and increased risk for acquired neurodegenerative diseases (e.g., Alzheimer's disease or Parkinson's disease) 2-5. Regardless of the severity of the damage caused to the brain tissue, a secondary sub-acute injury mechanism follows the initial injury involving the activation of resident microglia and infiltrating immune cells (such as neutrophils, monocytes, macrophages, lymphocytes etc.) that further contribute to neuroinflammation 6,7. Similarities between microglia and macrophages complicate research, and may often result in considering macrophages and microglia a uniform unit that acts in response to inflammatory stimuli 8,9. Methods for isolation of macrophages from non-CNS tissues are well established and as a result, macrophages are highly investigated. Despite sharing some functional activities with macrophages, it is not accurate to assume that microglia act in the same manner 10. Microglia play a crucial role in both healthy and injured brains. They are constantly active and survey the brain for signals, often acting to remove cellular debris 11. In normal conditions, microglia retain their ramified phenotype. Microglia activation occurs within minutes of injury or infection, resulting in a rapid change in gene expression. Activated microglia undergo dramatic morphological transformation 7 , which is required for their revised role in the neuroinflammatory response. Their newly acquired amoeboid shape makes them indistinguishable from the recruited blood derived macrophages responding...