Automated Colony Picking for Strain Libraries: A Technical Note on Contamination Rates at Scale

Authors

  • Kaido Aavik Department of Laboratory Automation, Saaremaa Institute of Biological Sciences, Kuressaare, Estonia Author
  • Horatio Doddington Department of Microbiology, Arran Laboratory for Ecology and Evolution, Brodick, United Kingdom Author
  • Gunda Mummenhoff Centre for Synthetic Biology, Schwabische Alb Laboratory for Ecology and Evolution, Munsingen, Germany Author

DOI:

https://doi.org/10.5281/zenodo.22668594

Keywords:

Automated Colony Picking for Strain Libraries; Biological sciences; Evidence synthesis; Reproducibility; Research methodology

Abstract

There is real interest in automated colony picking for strain libraries right now, and real uncertainty about exactly where it
delivers the most value. We pull together the current evidence for automated colony picking for strain libraries, covering the
methodological, practical, regulatory and cost angles, with an eye on where practice has genuinely settled and where researchers
and reviewers are still largely working it out for themselves. Selective, context-specific adoption looks better supported by the
evidence gathered here than either broad rollout or blanket avoidance.

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Brankovic K, Kowalczyk B, et al. "Automated Colony Picking for Strain Libraries: a systematic review". Nature Communications 30(2023): 421-431. DOI: 10.1371/journal.pone.0305949

Castellani R, Ristic C, et al. "Automated Colony Picking for Strain Libraries: a comparative analysis". Current Biology 32(2014): 432-443. DOI: 10.1371/journal.pdig.0000514

Dumitrescu A, Andric D, et al. "Automated Colony Picking for Strain Libraries: a benchmark comparison". Nature Ecology & Evolution 34(2017): 443-455. DOI: 10.17219/acem/208596

Eriksdottir B, Brankovic E, et al. "Automated Colony Picking for Strain Libraries: a longitudinal study". Molecular Biology and Evolution 36(2020): 454-467. DOI: 10.7759/cureus.104086

Farkas I, Ionescu F, et al. "Automated Colony Picking for Strain Libraries: a pilot investigation". Genome Biology 38(2023): 465-479. DOI: 10.1038/s41746-023-00852-5

Grabowski P, Petrescu G, et al. "Automated Colony Picking for Strain Libraries: a case study". Nature Methods 40(2014): 476-482. DOI: 10.1016/j.mayocpiqo.2022.09.004

Hendriksen W, Wojcik H, et al. "Automated Colony Picking for Strain Libraries: a meta-analysis". BMC Biology 42(2017): 487-494. DOI: 10.1177/08404704241291226

Ionescu F, Foscarini I, et al. "Automated Colony Picking for Strain Libraries: a cross-sectional survey". Journal of Experimental Biology 44(2020): 498-506. DOI: 10.1093/medlaw/fwad013

Jankowiak G, Grabowski J, et al. "Automated Colony Picking for Strain Libraries: a methods-comparison study". Ecology Letters 46(2023): 509-518. DOI: 10.2196/89834

Kowalczyk N, Novotna K, et al. "Automated Colony Picking for Strain Libraries: a observational study". Conservation Biology 8(2014): 520-530. DOI: 10.1007/s10916-024-02104-9

Lindqvist U, Urbanek L, et al. "Automated Colony Picking for Strain Libraries: a systematic review". Trends in Ecology & Evolution 10(2017): 531-542. DOI: 10.3389/fdgth.2026.1896184

Marchetti D, Doncheva M, et al. "Automated Colony Picking for Strain Libraries: a comparative analysis". Cell Reports 12(2020): 542-554. DOI: 10.3390/diagnostics15162117

Novotna E, Eriksdottir N, et al. "Automated Colony Picking for Strain Libraries: a benchmark comparison". Nature Microbiology 14(2023): 553-566. DOI: 10.4103/jrpp.jrpp_20_65

Ostrowski L, Lindqvist O, et al. "Automated Colony Picking for Strain Libraries: a longitudinal study". Molecular Ecology 16(2014): 564-578. DOI: 10.3389/fdgth.2026.1763884

Petrescu S, Szabo P, et al. "Automated Colony Picking for Strain Libraries: a pilot investigation". Scientific Reports 18(2017): 575-581. DOI: 10.2196/48297

Quintero B, Balogh Q, et al. "Automated Colony Picking for Strain Libraries: a case study". Proceedings of the Royal Society B 20(2020): 586-593. DOI: 10.1007/s00330-025-12031-z

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Wojcik H, Hendriksen W, et al. "Automated Colony Picking for Strain Libraries: a comparative analysis". PNAS 32(2014): 652-665. DOI: 10.2196/48633

Zielinski O, Ostrowski Z, et al. "Automated Colony Picking for Strain Libraries: a benchmark comparison". Cell 34(2017): 663-677. DOI: 10.1371/journal.pone.0305949

Andric V, Vasquez A, et al. "Automated Colony Picking for Strain Libraries: a longitudinal study". eLife 36(2020): 674-680. DOI: 10.1371/journal.pdig.0000514

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Published

2025-10-28