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ShareLoc — an open platform for sharing localization microscopy data

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Fig. 1: ShareLoc facilitates sharing, viewing, tagging and searching of SMLM data.

Data availability

All data used in this study are available on the ShareLoc platform (https://shareloc.xyz/#/?type=dataset&tags=) and on Zenodo (https://zenodo.org/communities/shareloc/?page=1&size=20), and each dataset has a unique DOI.

Code availability

The source code underlying the ShareLoc platform is available on Zenodo at https://doi.org/10.5281/zenodo.5045318 and on GitHub at https://github.com/imodpasteur/ShareLoc.XYZ/. Specifications and implementations of the *.smlm file format are available on Zenodo at https://zenodo.org/record/6576521 and on GitHub at https://github.com/imodpasteur/smlm-file-format/releases/tag/v0.2.0. Tools for batch download and to parse *.smlm are available on GitHub at https://github.com/imodpasteur/shareloc-utils#shareloc-utilities. Scripts used in Supplementary Fig. 1 to compare file sizes and downloading times are available at https://github.com/imodpasteur/smlm-file-format/tree/baiddd-patch-1/data/file_format_benchmark.

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Acknowledgements

We thank H. Harmse (EMBL-EBI) for help in linking ShareLoc to the EBI ontology lookup service; M. Schuetz and F. Woitzel for development and sharing of the potree and Fairy Dust viewers, respectively; M. Lelek for advice on metadata; J. Swedlow, J. Moore and S. Besson for stimulating several improvements of the platform. C.L. acknowledges funding from CNRS ATIP AO2016. S.F.H.B. and P.K. acknowledge funding support from Mechanobiology Institute seed funding, Singapore Ministry of Education (MOE2019-T2-2-014) and National Research Foundation (QEP-P7). M.K.S., M.M.C. and C.Z. acknowledge funding by Agence Nationale de la Recherche (grant ANR 17 CE13 0026 02) and M.M.C. by Labex DYNAMO (ANR-11-LABX-0011-DYNAMO) and MITOFUSION (ANR-19-CE11-0018). J.B., B.L. and C.Z. acknowledge funding by Institut Pasteur, by the Région Ile-de-France in the framework of DIM ELICIT, and by the Inception program (Investissement d’Avenir grant ANR-16-CONV-0005).

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Authors and Affiliations

Authors

Contributions

W.O. designed and implemented the ShareLoc platform. J.B. tested the platform, curated data, and wrote documentation. M.K.S., C.L., P.B., S.F.H.B., T.K., M.S., P.K., N.B., M.M.C. and B.L. provided SMLM data. C.Z. coordinated the project and wrote the manuscript with input and edits from W.O., J.B. and B.L. All authors read and approved the manuscript.

Corresponding authors

Correspondence to Wei Ouyang or Christophe Zimmer.

Ethics declarations

Competing interests

N.B. is shareholder of Abbelight. All other authors declare no competing interests.

Peer review

Peer review information

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

Supplementary information

Supplementary Information

Supplementary Notes 1 and 2; Supplementary Figures 1 and 2

Supplementary Software

ThunderSTORM plugin to import and export *.smlm files

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Ouyang, W., Bai, J., Singh, M.K. et al. ShareLoc — an open platform for sharing localization microscopy data. Nat Methods 19, 1331–1333 (2022). https://doi.org/10.1038/s41592-022-01659-0

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