Generation of Super-resolution Images from Barcode-based Spatial Transcriptomics Using Deep Image Prior

doi: https://doi.org/10.1016/j.crmeth.2024.100937

Abstract

Spatial transcriptomics (ST) has revolutionized the field of biology by providing a powerful tool for analyzing gene expression in situ. However, current ST methods, particularly barcode-based methods, have limitations in reconstructing high-resolution images from barcodes sparsely distributed in slides. Here, we present SuperST, a novel algorithm that enables the reconstruction of dense matrices from low-resolution ST libraries. SuperST based on deep image prior reconstructs spatial gene expression patterns as image matrices. SuperST allows gene expression mapping to better reflect immunofluorescence (IF) images. Compared with previous methods, SuperST generated output images that more closely resembled IF images for given gene expression maps. Additionally, SuperST overcomes the limitations inherent in IF images, highlighting its potential applications in the realm of spatial biology. By providing a more detailed understanding of gene expression in situ, SuperST has the potential to contribute to comprehensively understanding biology from various tissues.

Author

Park J, Cook S, Lee D, Choi J, Yoo S, Im H-J, Lee D, Choi H (2025).