Community-acquired pneumonia is an important clinical problem, with high rates of misdiagnosis and mortality. Diagnoses are typically conducted using two-dimensional chest x-rays, which have shown to be generally time-consuming and inaccurate, so current diagnostic methods should be improved. The goal of this research was to utilize Micro-Computed Tomography (MicroCT) and image analysis software to develop a diagnostic algorithm to quantitatively assess the severity of pneumonia in mice. This method provides immediate, more precise, and more accurate diagnoses as opposed to the qualitative assessments done by radiologists at present. MicroCT provides opportunities for non-invasive radiographic endpoints for pneumonia studies