Translational based medicine often utilizes animal models to study new and innovative therapeutics. In asthma and cystic fibrosis (CF), the animal models focus on airway inflammation and remodeling. The asthma model is based upon hypersensitivity induced airway disease whereas the CF model focuses on the inflammatory response to infection with Pseudomonas aeruginosa. Qualitative measures of inflammation and lung pathophysiology introduce significant variability and difficulty in interpreting interventional outcomes. This manuscript focuses on the development of a quantitative means to measure lung inflammation using the murine models of chronic asthma and CF. The highly sensitive and reproducible quantitative computational program interfaced with Image Pro Microscopy to monitor changes in lung inflammation and lung patho-physiology. The software-interfaces with image microscopy and automates the lung section review process. Results from this program recapitulated data obtained by manual point counting of inflammation, bronchoalveolar lavage differential and histology. The data shows a low coefficient of variation and high reproducibility between slides and sections. The utilization of this new microscopy program will enhance the quantitative means of establishing changes in lung structure and inflammation as a measure of therapeutic intervention with the ability of refining interpretation of in vivo models potentially short-circuiting translation into the clinical setting.