Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.


Graphing cell relations in spatial transcriptomics

A graph neural network-based tool is introduced to perform unsupervised cell clustering using spatially resolved transcriptomics data that can uncover cell identities, interactions, and spatial organization in tissues and organs.

Your institute does not have access to this article

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Overview of the graph-based model approach, processing SRT data from the human dorsolateral prefrontal cortex generated with 10x Visium7 as an example input.


  1. Li, J., Chen, S., Pan, X., Yuan, Y. & Shen, H.-B. Nat. Comput. Sci. (2022).

    Article  Google Scholar 

  2. Crosetto, N., Bienko, M. & van Oudenaarden, A. Nat. Rev. Genet. 16, 57–66 (2014).

    Article  Google Scholar 

  3. Burgess, D. J. Nat. Rev. Genet. 20, 317–317 (2019).

    Article  Google Scholar 

  4. Nat. Methods 18, 1 (2021).

  5. Xia, C., Fan, J., Emanuel, G., Hao, J. & Zhuang, X. Proc. Natl Acad. Sci. USA 116, 19490–19499 (2019).

    Article  Google Scholar 

  6. Eng, C. H. L. et al. Nature 568, 235–239 (2019).

    Article  Google Scholar 

  7. Maynard, K. R. et al. Nat. Neurosci. 24, 425–436 (2021).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations


Corresponding author

Correspondence to Xin Zhou.

Ethics declarations

Competing interests

The author declares no competing interests.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Zhou, X. Graphing cell relations in spatial transcriptomics. Nat Comput Sci 2, 354–355 (2022).

Download citation

  • Published:

  • Issue Date:

  • DOI:


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing