Super-resolved spatial transcriptomics by deep data fusion

Ludvig Bergenstråhle; Bryan Dawei He; Joseph Bergenstråhle; Xesús Manoel Abalo; Reza Mirzazadeh; Kim Thrane; Andrew L. Ji; Alma Andersson; Ludvig Larsson; Nathalie Stakenborg; Guy E. Boeckxstaens; Paul A. Khavari; James Zou; Joakim Lundeberg; Jonas Maaskola

doi:10.1038/s41587-021-01075-3

BioinformaticsNature BiotechnologyNov 29, 2021

Peer-reviewed journal article

Super-resolved spatial transcriptomics by deep data fusion

Ludvig Bergenstråhle iD, Bryan Dawei He iD, Joseph Bergenstråhle iD, Xesús Manoel Abalo iD, Reza Mirzazadeh iD, Kim Thrane iD, Andrew L. Ji iD, Alma Andersson iD, Ludvig Larsson iD, Nathalie Stakenborg iD, Guy E. Boeckxstaens iD, Paul A. Khavari iD, James Zou iD, Joakim Lundeberg iD, Jonas Maaskola iD

Abstract

In situ RNA capturing has made it possible to record histology and spatial gene expression from the same tissue section. Here, we introduce a method that combines data from both modalities to infer super-resolved full-transcriptome expression maps. Our method unravels transcriptional heterogeneity in micrometer-scale anatomical features and enables image-based in silico spatial transcriptomics without hybridization or sequencing.

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