Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software

Daniel Sage, Thanh An Pham, Hazen Babcock, Tomas Lukes, Thomas Pengo, Jerry Chao, Ramraj Velmurugan, Alex Herbert, Anurag Agrawal, Silvia Colabrese, Ann Wheeler, Anna Archetti, Bernd Rieger, Raimund Ober, Guy M. Hagen, Jean Baptiste Sibarita, Jonas Ries, Ricardo Henriques, Michael Unser, Seamus Holden

Research output: Contribution to journalArticle

47 Scopus citations

Abstract

With the widespread uptake of two-dimensional (2D) and three-dimensional (3D) single-molecule localization microscopy (SMLM), a large set of different data analysis packages have been developed to generate super-resolution images. In a large community effort, we designed a competition to extensively characterize and rank the performance of 2D and 3D SMLM software packages. We generated realistic simulated datasets for popular imaging modalities—2D, astigmatic 3D, biplane 3D and double-helix 3D—and evaluated 36 participant packages against these data. This provides the first broad assessment of 3D SMLM software and provides a holistic view of how the latest 2D and 3D SMLM packages perform in realistic conditions. This resource allows researchers to identify optimal analytical software for their experiments, allows 3D SMLM software developers to benchmark new software against the current state of the art, and provides insight into the current limits of the field.

Original languageEnglish (US)
Pages (from-to)387-395
Number of pages9
JournalNature Methods
Volume16
Issue number5
DOIs
StatePublished - May 1 2019

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't

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    Sage, D., Pham, T. A., Babcock, H., Lukes, T., Pengo, T., Chao, J., Velmurugan, R., Herbert, A., Agrawal, A., Colabrese, S., Wheeler, A., Archetti, A., Rieger, B., Ober, R., Hagen, G. M., Sibarita, J. B., Ries, J., Henriques, R., Unser, M., & Holden, S. (2019). Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software. Nature Methods, 16(5), 387-395. https://doi.org/10.1038/s41592-019-0364-4