Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation

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  • dc.contributor.author Cutler, Kevin J.
  • dc.contributor.author Stringer, Carsen
  • dc.contributor.author Lo, Teresa W.
  • dc.contributor.author Rappez, Luca
  • dc.contributor.author Stroustrup, Nicholas
  • dc.contributor.author Peterson, S. Brook
  • dc.contributor.author Wiggins, Paul A.
  • dc.contributor.author Mougous, Joseph D.
  • dc.date.accessioned 2023-01-18T07:35:19Z
  • dc.date.available 2023-01-18T07:35:19Z
  • dc.date.issued 2022
  • dc.description.abstract Advances in microscopy hold great promise for allowing quantitative and precise measurement of morphological and molecular phenomena at the single-cell level in bacteria; however, the potential of this approach is ultimately limited by the availability of methods to faithfully segment cells independent of their morphological or optical characteristics. Here, we present Omnipose, a deep neural network image-segmentation algorithm. Unique network outputs such as the gradient of the distance field allow Omnipose to accurately segment cells on which current algorithms, including its predecessor, Cellpose, produce errors. We show that Omnipose achieves unprecedented segmentation performance on mixed bacterial cultures, antibiotic-treated cells and cells of elongated or branched morphology. Furthermore, the benefits of Omnipose extend to non-bacterial subjects, varied imaging modalities and three-dimensional objects. Finally, we demonstrate the utility of Omnipose in the characterization of extreme morphological phenotypes that arise during interbacterial antagonism. Our results distinguish Omnipose as a powerful tool for characterizing diverse and arbitrarily shaped cell types from imaging data.
  • dc.description.sponsorship This work was supported by the National Institutes of Health (AI080609 to J.D.M., GM128191 to P.A.W., R01-GM128191 to T.W.L. and T32-GM008268 to K.J.C.). L.R. and N.S. were funded by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 852201), the Spanish Ministry of Economy, Industry and Competitiveness to the EMBL partnership, the Centro de Excelencia Severo Ochoa (CEX2020-001049-S, MCIN/AEI /10.13039/501100011033), the CERCA Programme/Generalitat de Catalunya and the Spanish Ministry of Economy, Industry and Competitiveness Excelencia award PID2020-115189GB-I00. C.S. was funded by the Howard Hughes Medical Institute at the Janelia Research Campus. J.D.M. is an HHMI Investigator.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Cutler KJ, Stringer C, Lo TW, Rappez L, Stroustrup N, Peterson SB, Wiggins PA, Mougous JD. Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation. Nat Methods. 2022 Nov;19(11):1438-48. DOI: 10.1038/s41592-022-01639-4
  • dc.identifier.doi http://dx.doi.org/10.1038/s41592-022-01639-4
  • dc.identifier.issn 1548-7091
  • dc.identifier.uri http://hdl.handle.net/10230/55327
  • dc.language.iso eng
  • dc.publisher Nature Research
  • dc.relation.ispartof Nat Methods. 2022 Nov;19(11):1438-48
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/852201
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2020-115189GB-I00
  • dc.rights © The Author(s) 2022. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword Bacteria
  • dc.subject.keyword Imaging
  • dc.title Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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