Segmentation of dense and multi-species bacterial colonies using models trained on synthetic microscopy images

Vincent Hickl; Abid Khan; René M. Rossi; Bruno F. B. Silva; Katharina Maniura-Weber

doi:10.1371/journal.pcbi.1012874

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Open Access

Peer-reviewed

Research Article

Segmentation of dense and multi-species bacterial colonies using models trained on synthetic microscopy images

Vincent Hickl ,

Roles Conceptualization, Formal analysis, Investigation, Methodology, Software, Visualization, Writing – original draft, Writing – review & editing

* E-mail: vincent.hickl@empa.ch

Affiliations Laboratory for Biointerfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland, Center for X-ray Analytics, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland, Laboratory for Biomimetic Membranes and Textiles, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland

https://orcid.org/0000-0003-2928-9568

⨯
Abid Khan,

Roles Conceptualization, Formal analysis, Investigation, Methodology, Software, Visualization, Writing – original draft, Writing – review & editing

Affiliations Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America, NASA Ames Research Center, Moffett Field, California, United States of America
⨯
René M. Rossi,

Roles Conceptualization, Funding acquisition, Supervision, Writing – review & editing

Affiliation Laboratory for Biomimetic Membranes and Textiles, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland

https://orcid.org/0000-0003-0946-682X

⨯
Bruno F. B. Silva,

Roles Conceptualization, Methodology, Supervision, Visualization, Writing – review & editing

Affiliations Laboratory for Biointerfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland, Center for X-ray Analytics, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland, Laboratory for Biomimetic Membranes and Textiles, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
⨯
Katharina Maniura-Weber

Roles Conceptualization, Funding acquisition, Supervision, Writing – review & editing

Affiliation Laboratory for Biointerfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
⨯

Segmentation of dense and multi-species bacterial colonies using models trained on synthetic microscopy images

Vincent Hickl,
Abid Khan,
René M. Rossi,
Bruno F. B. Silva,
Katharina Maniura-Weber

Published: April 4, 2025
https://doi.org/10.1371/journal.pcbi.1012874

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