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ShareLoc — an open platform for sharing localization microscopy data

Nature Methods volume 19, pages 1331–1333 (2022)Cite this article

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ShareLoc consists of (i) a storage service backed by Zenodo, a widely used open-access repository operated by CERN, and (ii) an extendable system of web plugins built upon ImJoy8, a state-of-the-art platform for developing and deploying interactive data science tools. With a Zenodo login, users can easily upload and store SMLM data (localizations and/or raw images up to 50 gigabytes) through the ShareLoc platform, automatically generating a digital object identifier (DOI) (Fig. 1b). Upon review and approval by a ShareLoc administrator, the new data will be shown on the ShareLoc website and available for download, visualization, export, and reanalysis7. Each dataset can be linked to other datasets or analysis tools, and by default SMLM data are linked to a dedicated viewer plugin (see below).

To facilitate rapid transmission of SMLM data, we developed a losslessly compressed binary file format (extension *.smlm) that substantially reduces localization file sizes and loading times, is portable, compact and flexible (for example, it can store arbitrary metadata), and is easily adjusted for 3D or multicolor data (Supplementary Note 1 and Supplementary Fig. 1a, b). Although ShareLoc uses the *.smlm format internally, the platform also supports the import of SMLM data in various standard formats and export as CSV files7, and has features for batch downloading and conversion of multiple datasets9 (see also Supplementary Software 1). Furthermore, we implemented a rapid WebGL-powered viewer plugin in ImJoy8, based on ‘potree’, a method designed for quick and fluid visualization of very large 3D point clouds that can handle billions of localizations and includes zooming, panning and rotation features7,10. This viewer is entirely browser-based, requires no installations or updates and operates across all operating systems, including mobile devices7 (Fig. 1c). Moreover, it allows quasi-instantaneous visualization without requiring download of the entire dataset, akin to Google Maps, thereby facilitating access for users with low Internet bandwidth7.

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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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Author notes

  1. Samuel F. H. Barnett

    Present address: Max Planck Institute for Medical Research, Heidelberg, Germany

  2. These authors contributed equally: Wei Ouyang, Jiachuan Bai.

Authors and Affiliations

  1. Imaging and Modeling Unit, Institut Pasteur, Université Paris Cité, Paris, France

    Wei Ouyang, Jiachuan Bai, Manish Kumar Singh, Benoît Lelandais & Christophe Zimmer

  2. Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH – Royal Institute of Technology, Stockholm, Sweden

    Wei Ouyang

  3. Sorbonne Université, Collège Doctoral, Paris, France

    Jiachuan Bai

  4. Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Sorbonne Université, CNRS, UMR8226, Institut de Biologie Physico-Chimique, Paris, France

    Manish Kumar Singh & Mickael M. Cohen

  5. Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France

    Christophe Leterrier

  6. Abbelight, Cachan, France

    Paul Barthelemy & Nicolas Bourg

  7. Mechanobiology Institute, National University of Singapore, Singapore, Singapore

    Samuel F. H. Barnett & Pakorn Kanchanawong

  8. Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore

    Samuel F. H. Barnett & Pakorn Kanchanawong

  9. Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Würzburg, Germany

    Teresa Klein & Markus Sauer

  10. Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France

    Benoît Lelandais

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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.

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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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