Retinopathic changes are common to many ocular diseases and if detected early, much of the change caused by various injuries can be prevented or in some cases reversed. However, detection and quantification of these changes currently requires tedious invasive and manual examination of retinal wholemount images. To remedy the quantitative limitations, we have designed a software system to automatically determine the vascular cell counts and coverage of retina in wholemount trypsin digest images. To verify the utility of the system, retinal trypsin digests from wild type (bcl-2 +/+) and bcl-2 deficient (bcl-2 -/-) mice were compared. Bcl-2 is a critical regulator of apoptosis with a significant role in retinal angiogenesis and vascularization. The bcl-2 -/- mice exhibited significant reduction in retinal vascular density and complexity. Thus, our results show the potential for automated evaluation of retinal trypsin digests delineating the differences between the wild type and bcl-2-deficient retinal vasculature.