Skip to main content

Thank you for visiting nature.com. 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.

  • News & Views
  • Published:

Spatial biology

Charting multicellular tissue structure cell-to-cell

Nature Genetics volume 56, pages 14–15 (2024)Cite this article

Subjects

The spatial biology revolution promises deep insights into tissue organization, but deriving this knowledge from diverse, complex data remains a major obstacle. Data-driven discovery of the multicellular organization of tissues is now achieved by transforming multimodal spatial imaging data using deep learning.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: CellCharter combines deep learning and spatial clustering to identify local niches.

References

  1. Hickey, J. W. et al. Nat. Methods 19, 284–295 (2022).

    Article  CAS  PubMed  Google Scholar 

  2. Vandereyken, K., Sifrim, A., Thienpont, B. & Voet, T. Nat. Rev. Genet. 24, 494–515 (2023).

    Article  CAS  PubMed  Google Scholar 

  3. Varrone, M. et al. Nat. Genet. https://doi.org/10.1038/s41588-023-01588-4 (2023).

    Article  PubMed  Google Scholar 

  4. Schürch, C. M. et al. Cell 182, 1341–1359.e19 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  5. Danenberg, E. et al. Nat. Genet. 54, 660–669 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Kim, J. et al. Nat. Methods 19, 1653–1661 (2022).

    Article  CAS  PubMed  Google Scholar 

  7. Kobayashi, H., Cheveralls, K. C., Leonetti, M. D. & Royer, L. A. Nat. Methods 19, 995–1003 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Dong, K. & Zhang, S. Nat. Commun. 13, 1739 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Fu, H. et al. Preprint at bioRxiv https://doi.org/10.1101/2021.06.15.448542 (2021).

  10. Goltsev, Y. et al. Cell 174, 968–981.e15 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Giesen, C. et al. Nat. Methods 11, 417–422 (2014).

    Article  CAS  PubMed  Google Scholar 

  12. He, S. et al. Nat. Biotechnol. 40, 1794–1806 (2022).

    Article  CAS  PubMed  Google Scholar 

  13. Zhang, M. et al. Nature 598, 137–143 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Wu, Z. et al. Nat. Biomed. Eng. 6, 1435–1448 (2022).

    Article  CAS  PubMed  Google Scholar 

  15. Wang, X. Q. et al. Nature 621, 868–876 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. CRUK Cambridge Institute, University of Cambridge, Cambridge, UK

    Ellen Schrader & H. Raza Ali

  2. Department of Histopathology, Addenbrookes Hospital, Cambridge, UK

    H. Raza Ali

Authors
  1. Ellen Schrader
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. H. Raza Ali
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to H. Raza Ali.

Ethics declarations

Competing interests

The authors declare no competing interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Schrader, E., Ali, H.R. Charting multicellular tissue structure cell-to-cell. Nat Genet 56, 14–15 (2024). https://doi.org/10.1038/s41588-023-01624-3

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41588-023-01624-3

Search

Advanced search

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