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In the past decade, single cell technologies have revolutionized our ability to study cellular heterogeneity. Spatial omics represents the next technological wave, granting spatial context to single cell transcriptomes. Integration analysis of transcripts and spatial information will greatly enable us to dissect tissue organization and inter-cellular communications. Here, we present SEDR, an unsupervised spatial embedded deep representation of both transcript and spatial information. The SEDRdoi:10.1101/2021.06.15.448542 fatcat:doit67j7bjawvlrspknv2qnyui