WebAtlas pipeline for integrated single-cell and spatial transcriptomic data

Tong Li^#¹, David Horsfall^#^{1

2}, Daniela Basurto-Lozada^#^{1

2}, Kenny Roberts¹, Martin Prete¹, John E G Lawrence¹, Peng He¹, Elisabeth Tuck¹, Josh Moore³, Aybuke Kupcu Yoldas⁴, Kolawole Babalola⁴, Matthew Hartley⁴, Shila Ghazanfar^{5

6}, Sarah A Teichmann^{1

7}, Muzlifah Haniffa^{8

9}, Omer Ali Bayraktar¹⁰

Affiliations

¹ Wellcome Sanger Institute, Hinxton, UK.
² Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
³ German BioImaging - Gesellschaft für Mikroskopie und Bildanalyse e.V., Konstanz, Germany.
⁴ European Bioinformatics Institute, Hinxton, UK.
⁵ School of Mathematics and Statistics, The University of Sydney, Sydney, New South Wales, Australia.
⁶ Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.
⁷ University of Cambridge, Cambridge, UK.
⁸ Wellcome Sanger Institute, Hinxton, UK. mh32@sanger.ac.uk.
⁹ Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK. mh32@sanger.ac.uk.
¹⁰ Wellcome Sanger Institute, Hinxton, UK. ob5@sanger.ac.uk.

^# Contributed equally.

PMID: 39160302
DOI: 10.1038/s41592-024-02371-x

WebAtlas pipeline for integrated single-cell and spatial transcriptomic data

Tong Li et al. Nat Methods. 2025 Jan.

. 2025 Jan;22(1):3-5.

doi: 10.1038/s41592-024-02371-x.

Authors

Affiliations

¹ Wellcome Sanger Institute, Hinxton, UK.
² Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
³ German BioImaging - Gesellschaft für Mikroskopie und Bildanalyse e.V., Konstanz, Germany.
⁴ European Bioinformatics Institute, Hinxton, UK.
⁵ School of Mathematics and Statistics, The University of Sydney, Sydney, New South Wales, Australia.
⁶ Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.
⁷ University of Cambridge, Cambridge, UK.
⁸ Wellcome Sanger Institute, Hinxton, UK. mh32@sanger.ac.uk.
⁹ Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK. mh32@sanger.ac.uk.
¹⁰ Wellcome Sanger Institute, Hinxton, UK. ob5@sanger.ac.uk.

^# Contributed equally.

PMID: 39160302
DOI: 10.1038/s41592-024-02371-x

No abstract available

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Conflict of interest statement

Competing interests: In the past three years, S.A.T. has consulted for or been a member of scientific advisory boards at Qiagen, Sanofi, GlaxoSmithKline and ForeSite Labs. She is a consultant and equity holder for TransitionBio and EnsoCell. J.M. holds equity in Glencoe Software, which builds products based on OME-NGFF. The remaining authors declare no competing interests.

References

1. zarr-developers/zarr-python: v2.17.1. https://doi.org/10.5281/zenodo.10790679 (2024).
1. Keller, M. S. et al. Preprint at OSF Preprints https://doi.org/10.31219/osf.io/y8thv (2021).
1. Kleshchevnikov, V. et al. Nat. Biotechnol. 40, 661–671 (2022). - DOI - PubMed
1. Ghazanfar, S., Guibentif, C. & Marioni, J. C. Nat. Biotechnol. 42, 284–292 (2024). - DOI - PubMed
1. Moore, J. et al. Histochem. Cell Biol. 160, 223–251 (2023). - DOI - PubMed - PMC

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WebAtlas pipeline for integrated single-cell and spatial transcriptomic data

Affiliations

WebAtlas pipeline for integrated single-cell and spatial transcriptomic data

Authors

Affiliations

Conflict of interest statement

References

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