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Machine learning tasks over image databases often generate masks that annotate image content (e.g., saliency maps, segmentation maps, depth maps) and enable a variety of applications (e.g., determine if a model is learning spurious correlations or if an image was maliciously modified to mislead a model). While queries that retrieve examples based on mask properties are valuable to practitioners, existing systems do not support them efficiently. In this paper, we formalize the problem and propose MaskSearch, a system that focuses on accelerating queries over databases of image masks while guaranteeing the correctness of query results. MaskSearch leverages a novel indexing technique and an efficient filter-verification query execution framework. Experiments with our prototype show that MaskSearch, using indexes approximately 5% of the compressed data size, accelerates individual queries by up to two orders of magnitude and consistently outperforms existing methods on various multi-query workloads that simulate dataset exploration and analysis processes.