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About 25\% of the world’s population live in informal urban settlements containing densely packed buildings (approximately 8,000 houses per $km^2$) which do not lend themselves favorably to state-of-the-art satellite-based building segmentation methods due to, for example, occlusion, vegetation, shadows and low resolution. To address these challenges, we introduce a novel instance segmentation and counting approach for dense buildings. Our system first extracts a conservative set of tentative building center points using a deep network for jumpstarting a Segment Anything Model 2 (SAM2) module to produce an initial over-segmentation. Second, we use a graph neural network to refine the over-segmented regions into polygons representing accurate building masks. Experiments show that our approach achieves higher accuracy in instance segmentation and counting especially in challenging densely packed buildings areas in Brazil, Mexico, India, Pakistan, and Kenya, for instance.