Purpose: Impaired insulin-induced microvascular recruitment in skeletal muscle contributes to insulin resistance in type 2 diabetic disease. Previously, quantification of microvascular recruitment at the capillary level has been performed with either the full image or manually selected region-of-interests. These subjective approaches are imprecise, time-consuming, and unsuitable for automated processes. Here, an automated multiscale image processing approach was performed by defining a vessel diameter threshold for an objective and reproducible analysis at the microvascular level. Approach: A population of C57BL/6J male mice fed standard chow and studied at age 13 to 16 weeks comprised the lean group and 24- to 31-week-old mice who received a high-fat diet were designated the obese group. A clinical ultrasound scanner (Acuson Sequoia 512) equipped with an 15L8-S linear array transducer was used in a nonlinear imaging mode for sensitive detection of an intravascular microbubble contrast agent. Results: By eliminating large vessels from the dynamic contrast-enhanced ultrasound (DCE-US) images (above in diameter), obesity-related changes in perfusion and morphology parameters were readily detected in the smaller vessels, which are known to have a greater impact on skeletal muscle glucose disposal. The results from the DCE-US images including all of the vessels were compared for three different-sized vessel groups, namely, vessels smaller than 300, 200, and in diameter. Conclusions: Our automated image processing provides objective and reproducible results by focusing on a particular size of vessel, thereby allowing for a selective evaluation of longitudinal changes in microvascular recruitment for a specific-sized vessel group between diseased and healthy microvascular networks.