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3D reconstruction of spatial expression

A novel approach to probabilistically align adjacent multiple tissue slices from spatially resolved transcriptomics data provides unprecedented depth for the investigation of tissue architecture and paves the way for new developments in 3D spatial analytics.

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Fig. 1: Aligning and integrating spatial transcriptomics data across adjacent slices.

References

  1. Zeira, R., Land, M. & Raphael, B. J. Nat. Methods https://doi.org/10.1038/s41592-022-01459-6 (2022).

    Article  PubMed  Google Scholar 

  2. Rao, A., Barkley, D., França, G. S. & Yanai, I. Nature 596, 211–220 (2021).

    Article  CAS  Google Scholar 

  3. Longo, S. K., Guo, M. G., Ji, A. L. & Khavari, P. A. Nat. Rev. Genet. 22, 627–644 (2021).

    Article  CAS  Google Scholar 

  4. Biancalani, T. et al. Nat. Methods 18, 1352–1362 (2021).

    Article  Google Scholar 

  5. Bergenstråhle, J., Larsson, L. & Lundeberg, J. BMC Genomics 21, 482 (2020).

    Article  Google Scholar 

  6. Anonymous. Nat. Methods 18, 1 (2021).

  7. Titouan, V., Courty, N., Tavenard, R., Laetitia, C. & Flamary, R. Optimal transport for structured data with application on graphs. in Proc. 36th Int. Conf. Machine Learning 97 (eds Chaudhuri, K. & Salakhutdinov, R.) 6275–6284 (2019).

  8. Rood, J. E. et al. Cell 179, 1455–1467 (2019).

    Article  CAS  Google Scholar 

  9. Andersson, A. et al. Preprint at bioRxiv https://doi.org/10.1101/2021.11.11.468178 (2021).

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Correspondence to Jean Y. H. Yang.

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Lin, Y., Yang, J.Y.H. 3D reconstruction of spatial expression. Nat Methods 19, 526–527 (2022). https://doi.org/10.1038/s41592-022-01476-5

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