MERFISH is a massively multiplexed single-molecule imaging technology for spatially resolved transcriptomics capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells.
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STAIG: Spatial transcriptomics analysis via image-aided graph contrastive learning
Spatial transcriptomics is an essential application for investigating cellular structures and interactions and requires multimodal information to precisely study spatial domains.Here, we propose STAIG, a deep-learning model that integrates gene expression, spatial coordinates, and histological images using graph-contrastive learning coupled with high-performance feature extraction. STAIG can integrate tissue slices without prealignment and remove batch effects. Moreover, it is designed to accept data acquired from various platforms, with or without histological images. By performing extensive benchmarks, we demonstrate the capability of STAIG to recognize spatial regions with high precision and uncover new insights into tumor microenvironments, highlighting its promising potential in deciphering spatial biological intricates.
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