Biomedical image mosaicking is a trending topic. It consists of computing a single large image from multiple observations and becomes a challenging task when said observations barely overlap or are subject to illumination changes, poor resolution, blur, or either highly textured or predominantly homogeneous content. Because such challenges are common in biomedical images, classical keypoint/feature-based methods perform poorly. In this paper, we propose a new framework based on pairwise template matching coupled with a constrained, confidence-driven global optimization strategy to solve the issue of microscopic biomedical image mosaicking. First we provide experimental results that show significant improvement on a subjective level. Then we describe a new validation strategy for objective assessment, which shows improvement as well.