BARcode DEmixing through Non-negative Spatial Regression (BarDensr)

• DOI: 10.1371/journal.pcbi.1008256
• Publication Date: 2021-03-08T18:41:38Z
• Authors: Shuonan Chen; Jackson Loper; Xiaoyin Chen; Alex Vaughan; Anthony M. Zador; Liam Paninski
• Keywords: genomics and proteomics; 0301 basic medicine; function; modification; QH301-705.5; RNA expression; bioinformatics; DNA; algorithms; 004; 03 medical and health sciences; computational biology; transcriptomes; gene expression; genetics & nucleic acid processing; Computer Simulation; Biology (General); RNA structure; Transcriptome; Algorithms; Spatial Regression; Research Article

Modern spatial transcriptomics methods can target thousands of different types of RNA transcripts in a single slice of tissue. Many biological applications demand a high spatial density of transcripts relative to the imaging resolution, leading to partial mixing of transcript rolonies in many voxels; unfortunately, current analysis methods do not perform robustly in this highly-mixed setting. Here we develop a new analysis approach, BARcode DEmixing through Non-negative Spatial Regression (BarDensr): we start with a generative model of the physical process that leads to the observed image data and then apply sparse convex optimization methods to estimate the underlying (demixed) rolony densities. We apply BarDensr to simulated and real data and find that it achieves state of the art signal recovery, particularly in densely-labeled regions or data with low spatial resolution. Finally, BarDensr is fast and parallelizable. We provide open-source code as well as an implementation for the ‘NeuroCAAS’ cloud platform.