BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis

BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis

Nature Genetics

10.1038/s41588-024-01664-3

http://dx.doi.org/10.1038/s41588-024-01664-3

Vipul Singhal, Nigel Chou, Joseph Lee, Yifei Yue, Jinyue Liu, Wan Kee Chock, Li Lin, Yun-Ching Chang, Erica Mei Ling Teo, Jonathan Aow, Hwee Kuan Lee, Kok Hao Chen, Shyam Prabhakar

27 February 2024

Singhal, V., Chou, N., Lee, J., Yue, Y., Liu, J., Chock, W. K., Lin, L., Chang, Y.-C., Teo, E. M. L., Aow, J., Lee, H. K., Chen, K. H., & Prabhakar, S. (2024). BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis. Nature Genetics, 56(3), 431–441. https://doi.org/10.1038/s41588-024-01664-3

AbstractSpatial omics data are clustered to define both cell types and tissue domains. We present Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an algorithm that unifies these two spatial clustering problems by embedding cells in a product space of their own and the local neighborhood transcriptome, representing cell state and microenvironment, respectively. BANKSY’s spatial feature augmentation strategy improved performance on both tasks when tested on diverse RNA (imaging, sequencing) and protein (imaging) datasets. BANKSY revealed unexpected niche-dependent cell states in the mouse brain and outperformed competing methods on domain segmentation and cell typing benchmarks. BANKSY can also be used for quality control of spatial transcriptomics data and for spatially aware batch effect correction. Importantly, it is substantially faster and more scalable than existing methods, enabling the processing of millions of cell datasets. In summary, BANKSY provides an accurate, biologically motivated, scalable and versatile framework for analyzing spatially resolved omics data.

Attribution 4.0 International (CC BY 4.0)

This research / project is supported by the A*STAR - Career Development Award
Grant Reference no. : 202D800010

This research / project is supported by the Singapore Ministry of Health’s National Medical Research Council - Open Fund - Young Individual Research Grant
Grant Reference no. : MOH-000239-00

This research / project is supported by the A*STAR - NA
Grant Reference no. : I1801E0029

This research / project is supported by the National Medical Research Council - Open Fund - Individual Research Grant
Grant Reference no. : OFIRG20nov-0056

This research / project is supported by the National Research Foundation - Competitive Research Programme
Grant Reference no. : NRF-CRP25-2020-0001

This research / project is supported by the A*STAR - IAF-PP
Grant Reference no. : H18/01/a0/020

This research / project is supported by the National Medical Research Council - Open Fund - Individual Research Grant
Grant Reference no. : OFIRG21jun-0090

https://oar.a-star.edu.sg/communities-collections/articles/20343

1546-1718
1061-4036

Genome Institute of Singapore

https://doi.org/10.1038/s41588-024-01664-3