Robust alignment of single-cell and spatial transcriptomes with CytoSPACE
Milad Rafiee VahidiD, Erin L. BrowniD, Chloé Beate SteeniD, Wubing ZhangiD, Hyun Soo JeoniD, Minji KangiD, Andrew J. GentlesiD, Aaron M. NewmaniD
Abstract
Recent studies have emphasized the importance of single-cell spatial biology, yet available assays for spatial transcriptomics have limited gene recovery or low spatial resolution. Here we introduce CytoSPACE, a method for aligning single-cell and spatial transcriptomes via convex linear optimization. Across diverse platforms and tissue types, we show that CytoSPACE outperforms previous methods with respect to noise-tolerance, accuracy, and efficiency, enabling improved analysis of spatial transcriptomics data at single-cell resolution.
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