Quantitative image analysis of microbial communities with BiofilmQ

Raimo Hartmann; Hannah Jeckel; Eric Jelli; Praveen K. Singh; Sanika Vaidya; Miriam Bayer; Daniel K. H. Rode; Lucia Vidakovic; Francisco Díaz-Pascual; Jiunn C. N. Fong; Anna Dragoš; Olga Lamprecht; Janne G. Thöming; Niklas Netter; Susanne Häussler; Carey D. Nadell; Victor Sourjik; Ákos T. Kovács; Fitnat H. Yildiz; Knut Drescher

doi:10.1038/s41564-020-00817-4

Quantitative image analysis of microbial communities with BiofilmQ

Raimo Hartmann, Hannah Jeckel, Eric Jelli, Praveen K. Singh, Sanika Vaidya, Miriam Bayer, Daniel K. H. Rode, Lucia Vidakovic, Francisco Díaz-Pascual, Jiunn C. N. Fong, Anna Dragoš, Olga Lamprecht, Janne G. Thöming, Niklas Netter, Susanne Häussler, Carey D. Nadell, Victor Sourjik, Ákos T. Kovács, Fitnat H. Yildiz, Knut Drescher^*

^*Corresponding author for this work

Research output: Contribution to journal › Journal article › Research › peer-review

9 Downloads (Pure)

Abstract

Biofilms are microbial communities that represent a highly abundant form of microbial life on Earth. Inside biofilms, phenotypic and genotypic variations occur in three-dimensional space and time; microscopy and quantitative image analysis are therefore crucial for elucidating their functions. Here, we present BiofilmQ—a comprehensive image cytometry software tool for the automated and high-throughput quantification, analysis and visualization of numerous biofilm-internal and whole-biofilm properties in three-dimensional space and time.

Original language	English
Journal	Nature Microbiology
Volume	6
Pages (from-to)	151-156
Number of pages	6
ISSN	2058-5276
DOIs	https://doi.org/10.1038/s41564-020-00817-4
Publication status	Published - 2021

Access to Document

10.1038/s41564-020-00817-4Licence: CC BY

FulltextFinal published version, 4.85 MBLicence: CC BY
Author correctionOther version, 756 KBLicence: CC BY

Fingerprint Dive into the research topics of 'Quantitative image analysis of microbial communities with BiofilmQ'. Together they form a unique fingerprint.

Cite this

Hartmann, R., Jeckel, H., Jelli, E., Singh, P. K., Vaidya, S., Bayer, M., Rode, D. K. H., Vidakovic, L., Díaz-Pascual, F., Fong, J. C. N., Dragoš, A., Lamprecht, O., Thöming, J. G., Netter, N., Häussler, S., Nadell, C. D., Sourjik, V., Kovács, Á. T., Yildiz, F. H., & Drescher, K. (2021). Quantitative image analysis of microbial communities with BiofilmQ. Nature Microbiology, 6, 151-156. https://doi.org/10.1038/s41564-020-00817-4

Hartmann, Raimo ; Jeckel, Hannah ; Jelli, Eric ; Singh, Praveen K. ; Vaidya, Sanika ; Bayer, Miriam ; Rode, Daniel K. H. ; Vidakovic, Lucia ; Díaz-Pascual, Francisco ; Fong, Jiunn C. N. ; Dragoš, Anna ; Lamprecht, Olga ; Thöming, Janne G. ; Netter, Niklas ; Häussler, Susanne ; Nadell, Carey D. ; Sourjik, Victor ; Kovács, Ákos T. ; Yildiz, Fitnat H. ; Drescher, Knut. / Quantitative image analysis of microbial communities with BiofilmQ. In: Nature Microbiology. 2021 ; Vol. 6. pp. 151-156.

@article{a49c55c29e164d56817a0c5eb421f608,

title = "Quantitative image analysis of microbial communities with BiofilmQ",

abstract = "Biofilms are microbial communities that represent a highly abundant form of microbial life on Earth. Inside biofilms, phenotypic and genotypic variations occur in three-dimensional space and time; microscopy and quantitative image analysis are therefore crucial for elucidating their functions. Here, we present BiofilmQ—a comprehensive image cytometry software tool for the automated and high-throughput quantification, analysis and visualization of numerous biofilm-internal and whole-biofilm properties in three-dimensional space and time.",

author = "Raimo Hartmann and Hannah Jeckel and Eric Jelli and Singh, {Praveen K.} and Sanika Vaidya and Miriam Bayer and Rode, {Daniel K. H.} and Lucia Vidakovic and Francisco D{\'i}az-Pascual and Fong, {Jiunn C. N.} and Anna Drago{\v s} and Olga Lamprecht and Th{\"o}ming, {Janne G.} and Niklas Netter and Susanne H{\"a}ussler and Nadell, {Carey D.} and Victor Sourjik and Kov{\'a}cs, {{\'A}kos T.} and Yildiz, {Fitnat H.} and Knut Drescher",

year = "2021",

doi = "10.1038/s41564-020-00817-4",

language = "English",

volume = "6",

pages = "151--156",

journal = "Nature Microbiology",

issn = "2058-5276",

publisher = "Nature Publishing Group",

}

Hartmann, R, Jeckel, H, Jelli, E, Singh, PK, Vaidya, S, Bayer, M, Rode, DKH, Vidakovic, L, Díaz-Pascual, F, Fong, JCN, Dragoš, A, Lamprecht, O, Thöming, JG, Netter, N, Häussler, S, Nadell, CD, Sourjik, V, Kovács, ÁT, Yildiz, FH & Drescher, K 2021, 'Quantitative image analysis of microbial communities with BiofilmQ', Nature Microbiology, vol. 6, pp. 151-156. https://doi.org/10.1038/s41564-020-00817-4

Quantitative image analysis of microbial communities with BiofilmQ. / Hartmann, Raimo; Jeckel, Hannah; Jelli, Eric; Singh, Praveen K.; Vaidya, Sanika; Bayer, Miriam; Rode, Daniel K. H.; Vidakovic, Lucia; Díaz-Pascual, Francisco; Fong, Jiunn C. N.; Dragoš, Anna; Lamprecht, Olga; Thöming, Janne G.; Netter, Niklas; Häussler, Susanne; Nadell, Carey D.; Sourjik, Victor; Kovács, Ákos T.; Yildiz, Fitnat H.; Drescher, Knut.

In: Nature Microbiology, Vol. 6, 2021, p. 151-156.

Research output: Contribution to journal › Journal article › Research › peer-review

TY - JOUR

T1 - Quantitative image analysis of microbial communities with BiofilmQ

AU - Hartmann, Raimo

AU - Jeckel, Hannah

AU - Jelli, Eric

AU - Singh, Praveen K.

AU - Vaidya, Sanika

AU - Bayer, Miriam

AU - Rode, Daniel K. H.

AU - Vidakovic, Lucia

AU - Díaz-Pascual, Francisco

AU - Fong, Jiunn C. N.

AU - Dragoš, Anna

AU - Lamprecht, Olga

AU - Thöming, Janne G.

AU - Netter, Niklas

AU - Häussler, Susanne

AU - Nadell, Carey D.

AU - Sourjik, Victor

AU - Kovács, Ákos T.

AU - Yildiz, Fitnat H.

AU - Drescher, Knut

PY - 2021

Y1 - 2021

N2 - Biofilms are microbial communities that represent a highly abundant form of microbial life on Earth. Inside biofilms, phenotypic and genotypic variations occur in three-dimensional space and time; microscopy and quantitative image analysis are therefore crucial for elucidating their functions. Here, we present BiofilmQ—a comprehensive image cytometry software tool for the automated and high-throughput quantification, analysis and visualization of numerous biofilm-internal and whole-biofilm properties in three-dimensional space and time.

AB - Biofilms are microbial communities that represent a highly abundant form of microbial life on Earth. Inside biofilms, phenotypic and genotypic variations occur in three-dimensional space and time; microscopy and quantitative image analysis are therefore crucial for elucidating their functions. Here, we present BiofilmQ—a comprehensive image cytometry software tool for the automated and high-throughput quantification, analysis and visualization of numerous biofilm-internal and whole-biofilm properties in three-dimensional space and time.

U2 - 10.1038/s41564-020-00817-4

DO - 10.1038/s41564-020-00817-4

M3 - Journal article

C2 - 33398098

VL - 6

SP - 151

EP - 156

JO - Nature Microbiology

JF - Nature Microbiology

SN - 2058-5276

ER -