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In order to engage in photosynthesis, leaves use pores on their surface - called stomata - to absorb CO₂. The opening of these pores results in the evaporation of H₂O, which is a detriment to leaf function. Thus a leaf is faced with the global optimization problem of maximizing CO₂ uptake for a fixed amount of H₂O loss. In solving this problem, stomata in spatially homogeneous patches often synchronize their apertures, even though this does not result in optimal local CO₂ uptake. In order to visualize these patches, a dye is injected into a leaf so that it fluoresces when closing its stomata. Understanding how synchronized patches of stomata results in an optimal CO₂ uptake for the entire leaf requires a thorough analysis of these fluorescence patterns. Using an experimental background model to drive video segmentation, we use a variational level-set approach for extracting the spatially synchronized stomatal patches from video taken of the leaf fluorescence. Methods of two-dimensional pattern analysis can then be used to analyze the dynamics of the stomatal patches.