In this paper, we address the analysis of 3D shape and shape change in non-rigid biological objects imaged via a stereo light microscope. We propose an integrated approach for the reconstruction of 3D structure and the motion analysis for images in which only a few informative features are available. The key components of this framework are: 1) image registration using a correlation-based approach, 2) region-of-interest extraction using motion-based segmentation, and 3) stereo and motion analysis using a cooperative spatial and temporal matching process. We describe these three stages of processing and illustrate the efficacy of the proposed approach using real images of a live frog's ventricle. The reconstructed dynamic 3D structure of the ventricle is demonstrated in our experimental results, and it agrees qualitatively with the observed images of the ventricle.