WebAtlas pipeline for integrated single-cell and spatial transcriptomic data

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).

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