Related Experiment Video
Updated: Jun 1, 2025
Isolation and Profiling of Human Primary Mesenteric Arterial Endothelial Cells at the Transcriptome Level
Published on: March 14, 2022
Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data
Jinming Cheng1,2, Xinyi Jin1,2, Gordon K Smyth3,4
1Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
Background:
Imaging-based spatial transcriptomics technologies allow us to explore spatial gene expression profiles at the cellular level. Cell type annotation of imaging-based spatial data is challenging due to the small gene panel, but it is a crucial step for downstream analyses. Many good reference-based cell type annotation tools have been developed for single-cell RNA sequencing and sequencing-based spatial transcriptomics data. However, the performance of the reference-based cell type annotation tools on imaging-based spatial transcriptomics data has not been well studied yet.
Results:
We compared performance of five reference-based methods (SingleR, Azimuth, RCTD, scPred and scmapCell) with the marker-gene-based manual annotation method on an imaging-based Xenium data of human breast cancer. A practical workflow has been demonstrated for preparing a high-quality single-cell RNA reference, evaluating the accuracy, and estimating the running time for reference-based cell type annotation tools.
Conclusions:
SingleR was the best performing reference-based cell type annotation tool for the Xenium platform, being fast, accurate and easy to use, with results closely matching those of manual annotation.
