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The Twenty Questions of bioimage object analysis

Nature Methods volume 20, pages 976–978 (2023)Cite this article

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The language used by microscopists who wish to find and measure objects in an image often differs in critical ways from that used by computer scientists who create tools to help them do this, making communication hard across disciplines. This work proposes a set of standardized questions that can guide analyses and shows how it can improve the future of bioimage analysis as a whole by making image analysis workflows and tools more FAIR (findable, accessible, interoperable and reusable).

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Fig. 1: The proposed questions and answers for the Twenty Questions of bioimage object analysis.

References

  1. Jamali, N., Dobson, E. T. A., Eliceiri, K. W., Carpenter, A. E. & Cimini, B. A. Biol. Imaging 1, e4 (2022).

  2. Paul-Gilloteaux, P. et al. F1000 Res. 10, 320 (2021).

    Article  Google Scholar 

  3. Sarkans, U. et al. Nat. Methods 18, 1418–1422 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Hammer, M. et al. Nat. Methods 18, 1427–1440 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Kalaš, M. et al. F1000 Res. https://doi.org/10.7490/f1000research.1117826.1 (2020).

    Article  Google Scholar 

  6. Jupp, S. et al. J. Biomed. Semantics 7, 28 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  7. Wilkinson, M. D. et al. Sci. Data 3, 160018 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  8. Barker, M. et al. Sci. Data 9, 622 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  9. Cimini, B. Zenodo https://doi.org/10.5281/zenodo.7654937 (2023).

  10. Stirling, D. R. et al. BMC Bioinformatics 22, 433 (2021).

  11. Haase, R. et al. FEBS Lett. 596, 2472–2485 (2022).

    Article  CAS  PubMed  Google Scholar 

  12. Schindelin, J., Rueden, C. T., Hiner, M. C. & Eliceiri, K. W. Mol. Reprod. Dev. 82, 518–529 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Schindelin, J. et al. Nat. Methods 9, 676–682 (2012).

    Article  CAS  PubMed  Google Scholar 

  14. Ulman, V. et al. Nat. Methods 14, 1141–1152 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Biaflows. https://biaflows-sandbox.neubias.org/#/ (accessed 19 February 2023).

  16. Grand Challenge. https://grand-challenge.org/ (accessed 19 February 2023).

  17. Rueden, C. T. et al. PLoS Biol. 17, e3000340 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  18. Schmied, C. et al. Community-developed checklists for publishing images and image analysis. Preprint at https://doi.org/10.48550/arXiv.2302.07005 (2023).

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Acknowledgements

The authors thank members of the Cimini lab, A. Carpenter and U. Manor for their feedback on the completeness of the schema. This work was supported by the US National Institutes of Health (NIH P41 GM135019 to B.A.C. and K.W.E.). B.A.C. (2020-225720) and K.W.E. also acknowledge funding from the Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation.

Author information

Authors and Affiliations

  1. Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Beth A. Cimini

  2. Center for Quantitative Cell Imaging, University of Wisconsin–Madison and Morgridge Institute for Research, Madison, WI, USA

    Kevin W. Eliceiri

Authors
  1. Beth A. Cimini
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  2. Kevin W. Eliceiri
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Contributions

B.A.C. drafted the initial schema, coded the web tool and wrote the manuscript; K.W.E. revised the schema and the manuscript.

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Correspondence to Beth A. Cimini.

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The authors declare no competing interests.

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

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Cimini, B.A., Eliceiri, K.W. The Twenty Questions of bioimage object analysis. Nat Methods 20, 976–978 (2023). https://doi.org/10.1038/s41592-023-01919-7

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