Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data

Cheng, J; Jin, X; Smyth, GK; Chen, Y

Author(s): Cheng, J; Jin, X; Smyth, GK; Chen, Y;
Details: Publication Year 2025-01-20,Volume 26,Issue #1,Page 22
Journal Title: BMC Bioinformatics
Abstract: 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.
Publisher: BMC
Keywords: Humans; *Benchmarking; *Single-Cell Analysis/methods; Gene Expression Profiling/methods; Transcriptome/genetics; Breast Neoplasms/genetics; Sequence Analysis, RNA/methods; Female; Molecular Sequence Annotation/methods; Software; Cell type annotation; Imaging-based; Reference-based annotation; Single-cell; Spatial transcriptomics; Xenium
Research Division(s): Bioinformatics and Computational Biology
PubMed ID: 39833693
Publisher's Version: https://doi.org/10.1186/s12859-025-06044-0
Open Access at Publisher's Site: https://doi.org/10.1186/s12859-025-06044-0.
Terms of Use/Rights Notice: Refer to copyright notice on published article.
Documents: s12859-025-06044-0.pdf - (6.51MB, application/pdf)

Creation Date: 2025-02-07 11:22:04

Last Modified: 2025-02-07 11:29:47