WebAtlas pipeline for integrated single-cell and spatial transcriptomic data

All software code has been made publicly available on GitHub at https://github.com/haniffalab/webatlas-pipeline. Each software release is permanently archived on Zenodo at https://doi.org/10.5281/zenodo.7405818. Comprehensive documentation, tutorials and sample workflows are available at https://haniffalab.github.io/webatlas-pipeline.

We thank the authors of the human lower limb atlas study for sharing data, Sébastien Besson for consultation on use of OME-NGFF as a common format, Pavel Mazin for help with Cell2location analysis of the lower limb Visium data, Sanger Institute’s Informatics and Digital Solutions team for infrastructure support for hosting the datasets and website, and Jason Swedlow for comments on the manuscript. This work was funded by Wellcome Trust core funding (206194 and 220540/Z/20/A) and Strategic Science Award (221052/Z/20/Z, 221052/A/20/Z, 221052/B/20/Z, 221052/C/20/Z and 221052/E/20/Z) to M.H. and O.A.B., and a Wellcome Trust Senior Research Fellowship Award (223092/Z/21/Z) to M.H. J.M. was supported for work on OME-NGFF by grant numbers 2019-207272 and 2022-310144 and on Zarr by grant numbers 2019-207338 and 2021-237467 from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation, and was funded by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) 501864659 as part of NFDI4BIOIMAGE. S.G was supported for work on StabMap imputation by an Australian Research Council Discovery Early Career Researcher Award (DE220100964) funded by the Australian Government and a Chan Zuckerberg Initiative Single Cell Biology Data Insights grant (2022-249319).

1. These authors contributed equally: Tong Li, David Horsfall, Daniela Basurto-Lozada.

2. These authors jointly supervised this work: Muzlifah Haniffa, Omer Ali Bayraktar.

Authors and Affiliations

1. Wellcome Sanger Institute, Hinxton, UK

   Tong Li, David Horsfall, Daniela Basurto-Lozada, Kenny Roberts, Martin Prete, John E. G. Lawrence, Peng He, Elisabeth Tuck, Sarah A. Teichmann, Muzlifah Haniffa & Omer Ali Bayraktar

2. Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK

   David Horsfall, Daniela Basurto-Lozada & Muzlifah Haniffa

3. German BioImaging – Gesellschaft für Mikroskopie und Bildanalyse e.V., Konstanz, Germany

   Josh Moore

4. European Bioinformatics Institute, Hinxton, UK

   Aybuke Kupcu Yoldas, Kolawole Babalola & Matthew Hartley

5. School of Mathematics and Statistics, The University of Sydney, Sydney, New South Wales, Australia

   Shila Ghazanfar

6. Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia

   Shila Ghazanfar

7. University of Cambridge, Cambridge, UK

   Sarah A. Teichmann

Contributions

T.L., D.H., D.B.L., M.H. and O.A.B. conceived the study. T.L., D.H. and D.B.L developed the WebAtlas pipeline and processed the sample datasets. M.P. supported WebAtlas implementation. J.E.G.L., P.H. and S.T. shared limb scRNA-seq and Visium data and contributed to limb data interpretation. K.R., E.T. and S.G. contributed to limb ISS data interpretation. A.K.Y., K.B. and M.H. assisted with BioImage Archive submission of limb datasets. J.M. consulted on the OME-Zarr specifications and reviewed and edited the manuscript. T.L., D.H., D.B.L., M.H. and O.A.B. wrote the manuscript with feedback from all authors.

Corresponding authors

Correspondence to Muzlifah Haniffa or Omer Ali Bayraktar.

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.

Peer review information

Nature Methods thanks Nils Gehlenborg and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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