We propose an image processing pipeline for dendritic spine detection in two-photon fluorescence microscopy images. Spines of interest to neuroscientists often contain high intensity regions with respect to their surroundings. We find such maxima regions using morphological image reconstruction. These regions facilitate a multi-level segmentation algorithm to detect spines. First, watershed algorithm is applied to extract initial rough regions of spines. Then, these results are further refined using a graph-theoretic region-growing algorithm which incorporates segmentation on a sparse representation of image data and hierarchical clustering as a post-processing step. We compare our final results to segmentation results of the domain expert. Our pipeline produces promising segmentation results with practical run times for monitoring streaming data.